1VQ9: CCA-PHE-CAP-BIO and the antibiotic sparsomycin
The structure of CCA-PHE-CAP-BIO and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui. Determined by X-ray diffraction at 2.4 Å resolution. Released 29 Nov 2005.
- Method
- X-ray diffraction
- Resolution
- 2.4 Å
- Organism
- Haloarcula marismortui
- Chains
- 32
- Atoms
- 98,979
- Mol. weight
- 1490.37 kDa
- Ligands
- MG, SR, SPS, CD
- Released
- 29 Nov 2005
Explore 1VQ9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1VQ9 contains 184 α-helices and 198 β-strands across 29 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain 1: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-8 | 4 | |
| β-strand | 16-18 | 3 | 4 |
| β-strand | 25-28 | 4 | 4 |
| β-strand | 33-34 | 2 | 4 |
| α-helix | 45-46 | 2 | |
| α-helix | 49-51 | 3 | |
Chain 2: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-17 | 13 | |
| α-helix | 20-22 | 3 | |
| α-helix | 23-29 | 7 | |
Chain 3: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 14 |
| β-strand | 6-11 | 6 | 15 |
| β-strand | 16-24 | 9 | 15 |
| α-helix | 26-30 | 5 | |
| α-helix | 35-42 | 8 | |
| α-helix | 50-53 | 4 | |
| β-strand | 64 | 1 | 16 |
| β-strand | 67-71 | 5 | 15 |
| β-strand | 77-78 | 2 | 15 |
| β-strand | 84 | 1 | 16 |
| β-strand | 89-91 | 3 | 14 |
Chain A: 10 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-10 | 6 | |
| α-helix | 14-16 | 3 | |
| α-helix | 20-22 | 3 | |
| α-helix | 28-30 | 3 | |
| β-strand | 39-48 | 10 | 5 |
| β-strand | 53-60 | 8 | 5 |
| β-strand | 64-69 | 6 | 5 |
| β-strand | 71 | 1 | 6 |
| β-strand | 75 | 1 | 3 |
| β-strand | 79-81 | 3 | 5 |
| β-strand | 82 | 1 | 7 |
| β-strand | 93-95 | 3 | 7 |
| α-helix | 96-98 | 3 | |
| α-helix | 100 | 1 | |
| β-strand | 104-106 | 3 | 7 |
| β-strand | 108 | 1 | 8 |
| β-strand | 118 | 1 | 8 |
| β-strand | 126-128 | 3 | 7 |
| β-strand | 136-139 | 4 | 7 |
| β-strand | 145-148 | 4 | 7 |
| β-strand | 153-156 | 4 | 7 |
| β-strand | 159 | 1 | 6 |
| α-helix | 172-179 | 8 | |
| α-helix | 191-193 | 3 | |
| α-helix | 196-198 | 3 | |
| β-strand | 214-215 | 2 | 9 |
| α-helix | 219-220 | 2 | |
| β-strand | 227-228 | 2 | 9 |
Chain B: 9 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-31 | 2 | |
| β-strand | 37-38 | 2 | 10 |
| β-strand | 41-54 | 14 | 11 |
| β-strand | 66-75 | 10 | 11 |
| β-strand | 79-90 | 12 | 10 |
| β-strand | 93-101 | 9 | 10 |
| α-helix | 109-111 | 3 | |
| α-helix | 121-134 | 14 | |
| β-strand | 137-145 | 9 | 10 |
| α-helix | 148-150 | 3 | |
| β-strand | 161-167 | 7 | 10 |
| α-helix | 171-184 | 14 | |
| β-strand | 187-188 | 2 | 10 |
| β-strand | 199-205 | 7 | 11 |
| α-helix | 206-207 | 2 | |
| β-strand | 208-212 | 5 | 12 |
| α-helix | 214-218 | 5 | |
| α-helix | 220-223 | 4 | |
| α-helix | 225-228 | 4 | |
| β-strand | 255-258 | 4 | 12 |
| β-strand | 261-275 | 15 | 11 |
| β-strand | 284 | 1 | 13 |
| β-strand | 288 | 1 | 13 |
| β-strand | 292-298 | 7 | 11 |
| β-strand | 308-313 | 6 | 11 |
| β-strand | 327-330 | 4 | 11 |
Chain C: 13 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 17 |
| β-strand | 12-17 | 6 | 17 |
| α-helix | 20-23 | 4 | |
| α-helix | 25-26 | 2 | |
| α-helix | 28-40 | 13 | |
| α-helix | 43-45 | 3 | |
| β-strand | 59 | 1 | 18 |
| β-strand | 72-73 | 2 | 18 |
| β-strand | 76-77 | 2 | 18 |
| α-helix | 104-117 | 14 | |
| α-helix | 121-127 | 7 | |
| β-strand | 138-140 | 3 | 17 |
| α-helix | 142-146 | 5 | |
| α-helix | 150-158 | 9 | |
| α-helix | 164-168 | 5 | |
| β-strand | 173-174 | 2 | 19 |
| α-helix | 178-182 | 5 | |
| β-strand | 186-187 | 2 | 19 |
| β-strand | 193-196 | 4 | 17 |
| β-strand | 211-214 | 4 | 17 |
| α-helix | 220-223 | 4 | |
| α-helix | 225-227 | 3 | |
| β-strand | 233-236 | 4 | 17 |
| α-helix | 237-243 | 7 | |
Chain D: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-24 | 7 | 21 |
| α-helix | 38-44 | 7 | |
| β-strand | 50-52 | 3 | 21 |
| β-strand | 58 | 1 | 22 |
| β-strand | 62 | 1 | 22 |
| β-strand | 70-75 | 6 | 21 |
| α-helix | 78-87 | 10 | |
| α-helix | 88-90 | 3 | |
| β-strand | 98 | 1 | 21 |
| β-strand | 104-106 | 3 | 21 |
| β-strand | 129-134 | 6 | 21 |
| α-helix | 137-142 | 6 | |
| α-helix | 150-152 | 3 | |
| α-helix | 153-155 | 3 | |
| α-helix | 159-167 | 9 | |
Chain E: 6 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 23 |
| β-strand | 12-16 | 5 | 24 |
| β-strand | 19-24 | 6 | 24 |
| β-strand | 27-32 | 6 | 24 |
| β-strand | 39-43 | 5 | 23 |
| β-strand | 46-50 | 5 | 23 |
| α-helix | 56-77 | 22 | |
| β-strand | 80-87 | 8 | 25 |
| α-helix | 92-93 | 2 | |
| β-strand | 94-97 | 4 | 26 |
| β-strand | 101-105 | 5 | 26 |
| α-helix | 107-109 | 3 | |
| α-helix | 113 | 1 | |
| β-strand | 114-117 | 4 | 26 |
| α-helix | 118-119 | 2 | |
| β-strand | 123-127 | 5 | 25 |
| β-strand | 130-135 | 6 | 25 |
| α-helix | 138-150 | 13 | |
| β-strand | 165-170 | 6 | 25 |
21 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| 23S ribosomal rna | 0 | RNA | 2922 | Haloarcula marismortui | |
| 5S ribosomal RNA | 9 | RNA | 122 | Haloarcula marismortui | |
| 5'-r(*cp*cp*ap*(phe)*(aca))-3' | 4 | RNA | 5 | | |
| 50S ribosomal protein L2P | A | protein | 240 | Haloarcula marismortui | P20276 (AlphaFold model) |
| 50S ribosomal protein L3P | B | protein | 338 | Haloarcula marismortui | P20279 (AlphaFold model) |
| 50S ribosomal protein L4E | C | protein | 246 | Haloarcula marismortui | P12735 (AlphaFold model) |
| 50S ribosomal protein L5P | D | protein | 177 | Haloarcula marismortui | P14124 (AlphaFold model) |
| 50S ribosomal protein L6P | E | protein | 178 | Haloarcula marismortui | P14135 |
| 50S ribosomal protein L7AE | F | protein | 120 | Haloarcula marismortui | P12743 |
| Acidic ribosomal protein P0 homolog | G | protein | 348 | Haloarcula marismortui | P15825 |
| 50S ribosomal protein L10E | H | protein | 171 | Haloarcula marismortui | P60617 |
| 50S ribosomal protein L13P | J | protein | 145 | Haloarcula marismortui | P29198 |
20 more molecules are not listed.
Sequence of entity 1 (0), FASTA
>1VQ9_1 23S ribosomal rna (chains 0)
UUGGCUACUAUGCCAGCUGGUGGAUUGCUCGGCUCAGGCGCUGAUGAAGGACGUGCCAAG
CUGCGAUAAGCCAUGGGGAGCCGCACGGAGGCGAAGAACCAUGGAUUUCCGAAUGAGAAU
CUCUCUAACAAUUGCUUCGCGCAAUGAGGAACCCCGAGAACUGAAACAUCUCAGUAUCGG
GAGGAACAGAAAACGCAAUGUGAUGUCGUUAGUAACCGCGAGUGAACGCGAUACAGCCCA
AACCGAAGCCCUCACGGGCAAUGUGGUGUCAGGGCUACCUCUCAUCAGCCGACCGUCUCG
ACGAAGUCUCUUGGAACAGAGCGUGAUACAGGGUGACAACCCCGUACUCGAGACCAGUAC
GACGUGCGGUAGUGCCAGAGUAGCGGGGGUUGGAUAUCCCUCGCGAAUAACGCAGGCAUC
GACUGCGAAGGCUAAACACAACCUGAGACCGAUAGUGAACAAGUAGUGUGAACGAACGCU
GCAAAGUACCCUCAGAAGGGAGGCGAAAUAGAGCAUGAAAUCAGUUGGCGAUCGAGCGAC
AGGGCAUACAAGGUCCCUCGACGAAUGACCGACGCGCGAGCGUCCAGUAAGACUCACGGG
AAGCCGAUGUUCUGUCGUACGUUUUGAAAAACGAGCCAGGGAGUGUGUCUGCAUGGCAAG
UCUAACCGGAGUAUCCGGGGAGGCACAGGGAAACCGACAUGGCCGCAGGGCUUUGCCCGA
GGGCCGCCGUCUUCAAGGGCGGGGAGCCAUGUGGACACGACCCGAAUCCGGACGAUCUAC
GCAUGGACAAGAUGAAGCGUGCCGAAAGGCACGUGGAAGUCUGUUAGAGUUGGUGUCCUA
CAAUACCCUCUCGUGAUCUAUGUGUAGGGGUGAAAGGCCCAUCGAGUCCGGCAACAGCUG
GUUCCAAUCGAAACAUGUCGAAGCAUGACCUCCGCCGAGGUAGUCUGUGAGGUAGAGCGA
CCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAG
ACGCCGUUUGACGCGGGGAUUCCGGUGCGCGGGGUAAGCCUGUGUACCAGGAGGGGAACA
ACCCAGAGAUAGGUUAAGGUCCCCAAGUGUGGAUUAAGUGUAAUCCUCUGAAGGUGGUCU
CGAGCCCUAGACAGCCGGGAGGUGAGCUUAGAAGCAGCUACCCUCUAAGAAAAGCGUAAC
AGCUUACCGGCCGAGGUUUGAGGCGCCCAAAAUGAUCGGGACUCAAAUCCACCACCGAGA
CCUGUCCGUACCACUCAUACUGGUAAUCGAGUAGAUUGGCGCUCUAAUUGGAUGGAAGUA
GGGGUGAAAACUCCUAUGGACCGAUUAGUGACGAAAAUCCUGGCCAUAGUAGCAGCGAUA
GUCGGGUGAGAACCCCGACGGCCUAAUGGAUAAGGGUUCCUCAGCACUGCUGAUCAGCUG
AGGGUUAGCCGGUCCUAAGUCAUACCGCAACUCGACUAUGACGAAAUGGGAAACGGGUUA
AUAUUCCCGUGCCACUAUGCAGUGAAAGUUGACGCCCUGGGGUCGAUCACGCUGGGCAUU
CGCCCAGUCGAACCGUCCAACUCCGUGGAAGCCGUAAUGGCAGGAAGCGGACGAACGGCG
GCAUAGGGAAACGUGAUUCAACCUGGGGCCCAUGAAAAGACGAGCAUAGUGUCCGUACCG
AGAACCGACACAGGUGUCCAUGGCGGCGAAAGCCAAGGCCUGUCGGGAGCAACCAACGUU
AGGGAAUUCGGCAAGUUAGUCCCGUACCUUCGGAAGAAGGGAUGCCUGCUCCGGAACGGA
GCAGGUCGCAGUGACUCGGAAGCUCGGACUGUCUAGUAACAACAUAGGUGACCGCAAAUC
CGCAAGGACUCGUACGGUCACUGAAUCCUGCCCAGUGCAGGUAUCUGAACACCUCGUACA
AGAGGACGAAGGACCUGUCAACGGCGGGGGUAACUAUGACCCUCUUAAGGUAGCGUAGUA
CCUUGCCGCAUCAGUAGCGGCUUGCAUGAAUGGAUUAACCAGAGCUUCACUGUCCCAACG
UUGGGCCCGGUGAACUGUACAUUCCAGUGCGGAGUCUGGAGACACCCAGGGGGAAGCGAA
GACCCUAUGGAGCUUUACUGCAGGCUGUCGCUGAGACGUGGUCGCCGAUGUGCAGCAUAG
GUAGGAGACACUACACAGGUACCCGCGCUAGCGGGCCACCGAGUCAACAGUGAAAUACUA
CCCGUCGGUGACUGCGACUCUCACUCCGGGAGGAGGACACCGAUAGCCGGGCAGUUUGAC
UGGGGCGGUACGCGCUCGAAAAGAUAUCGAGCGCGCCCUAUGGCUAUCUCAGCCGGGACA
GAGACCCGGCGAAGAGUGCAAGAGCAAAAGAUAGCUUGACAGUGUUCUUCCCAACGAGGA
ACGCUGACGCGAAAGCGUGGUCUAGCGAACCAAUUAGCCUGCUUGAUGCGGGCAAUUGAU
GACAGAAAAGCUACCCUAGGGAUAACAGAGUCGUCACUCGCAAGAGCACAUAUCGACCGA
GUGGCUUGCUACCUCGAUGUCGGUUCCCUCCAUCCUGCCCGUGCAGAAGCGGGCAAGGGU
GAGGUUGUUCGCCUAUUAAAGGAGGUCGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUC
GGCUGCUAUCUACUGGGUGUGUAAUGGUGUCUGACAAGAACGACCGUAUAGUACGAGAGG
AACUACGGUUGGUGGCCACUGGUGUACCGGUUGUUCGAGAGAGCACGUGCCGGGUAGCCA
CGCCACACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACAC
CGCCGAGGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAAC
GAGACGUUAAGCCCACGAGCACUAACAGACCAAAGCCAUCAU
Sequence of entity 2 (9), FASTA
>1VQ9_2 5S ribosomal RNA (chains 9)
UUAGGCGGCCACAGCGGUGGGGUUGCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCC
CACCAGCGUUCCGGGGAGUACUGGAGUGCGCGAGCCUCUGGGAAACCCGGUUCGCCGCCA
CC
Sequence of entity 3 (4), FASTA
>1VQ9_3 5'-R(*CP*CP*AP*(PHE)*(ACA))-3' (chains 4)
CCAFX
Sequence of entity 4 (A), FASTA
>1VQ9_4 50S ribosomal protein L2P (chains A)
MGRRIQGQRRGRGTSTFRAPSHRYKADLEHRKVEDGDVIAGTVVDIEHDPARSAPVAAVE
FEDGDRRLILAPEGVGVGDELQVGVSAEIAPGNTLPLAEIPEGVPVCNVESSPGDGGKFA
RASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVAGGGRTDKPFVKAGNKHHKM
KARGTKWPNVRGVAMNAVDHPFGGGGRQHPGKPKSISRNAPPGRKVGDIASKRTGRGGNE
Sequence of entity 5 (B), FASTA
>1VQ9_5 50S ribosomal protein L3P (chains B)
MPQPSRPRKGSLGFGPRKRSTSETPRFNSWPSDDGQPGVQGFAGYKAGMTHVVLVNDEPN
SPREGMEETVPVTVIETPPMRAVALRAYEDTPYGQRPLTEVWTDEFHSELDRTLDVPEDH
DPDAAEEQIRDAHEAGDLGDLRLITHTVPDAVPSVPKKKPDVMETRVGGGSVSDRLDHAL
DIVEDGGEHAMNDIFRAGEYADVAGVTKGKGTQGPVKRWGVQKRKGKHARQGWRRRIGNL
GPWNPSRVRSTVPQQGQTGYHQRTELNKRLIDIGEGDEPTVDGGFVNYGEVDGPYTLVKG
SVPGPDKRLVRFRPAVRPNDQPRLDPEVRYVSNESNQG
Sequence of entity 6 (C), FASTA
>1VQ9_6 50S ribosomal protein L4E (chains C)
MQATIYDLDGNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAES
FGSGRGQAHVPKLDGRARRVPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATAD
ADLVADRGHEFDRDEVPVVVSDDFEDLVKTQEVVSLLEALDVHADIDRADETKIKAGQGS
ARGRKYRRPASILFVTSDEPSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESAL
AEVAER
Sequence of entity 7 (D), FASTA
>1VQ9_7 50S ribosomal protein L5P (chains D)
MSSESESGGDFHEMREPRIEKVVVHMGIGHGGRDLANAEDILGEITGQMPVRTKAKRTVG
EFDIREGDPIGAKVTLRDEMAEEFLQTALPLAELATSQFDDTGNFSFGVEEHTEFPSQEY
DPSIGIYGLDVTVNLVRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEVSE
Sequence of entity 8 (E), FASTA
>1VQ9_8 50S ribosomal protein L6P (chains E)
MPRVELEIPEDVDAEQDHLDITVEGDNGSVTRRLWYPDIDVSVDGDTVVIESDEDNAKTM
STIGTFQSHIENMFHGVTEGWEYGMEVFYSHFPMQVNVEGDEVVIENFLGEKAPRRTTIH
GDTDVEIDGEELTVSGPDIEAVGQTAADIEQLTRINDKDVRVFQDGVYITRKPNRGDA
Sequence of entity 9 (F), FASTA
>1VQ9_9 50S ribosomal protein L7AE (chains F)
MPVYVDFDVPADLEDDALEALEVARDTGAVKKGTNETTKSIERGSAELVFVAEDVQPEEI
VMHIPELADEKGVPFIFVEQQDDLGHAAGLEVGSAAAAVTDAGEADADVEDIADKVEELR
Sequence of entity 10 (G), FASTA
>1VQ9_10 ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG (chains G)
MSAESERKTETIPEWKQEEVDAIVEMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELR
VSRNTLLERALDDVDDGLEDLNGYITGQVGLIGTDDNPFSLFQELEASKTPAPIGAGEVA
PNDIVIPEGDTGVDPGPFVGELQSVGADARIQEGSIQVLSDSTVLDTGEEVSQELSNVLN
ELGIEPKEVGLDLRAVFADGVLFEPEELELDIDEYRSDIQAAAGRAFNLSVNADYPTATT
APTMLQSDRGNAKSLALQAAIEDPEVVPDLVSKADAQVRALASQIDDEEALPEELQGVEA
DVATEEPTDDQDDDTASEDDADADDAAEEADDDDDDDEDAGDALGAMF
Sequence of entity 11 (H), FASTA
>1VQ9_11 50S RIBOSOMAL PROTEIN L10E (chains H)
KPASMYRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQLRHG
SLEASRLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVSDGMRAAFGKI
VGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIDSSPAGNA
Sequence of entity 12 (J), FASTA
>1VQ9_12 50S ribosomal protein L13P (chains J)
MSVAEFDADVIVDARDCIMGRVASQVAEQALDGETVAVVNAERAVITGREEQIVEKYEKR
VDIGNDNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYDEDGEVLDGTS
LDRLSNIKFVTLGEISETLGANKTW
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 94 |
| SR | Strontium ion | Sr | 114 |
| SPS | Sparsomycin | C13 H19 N3 O5 S2 | 1 |
| CD | Cadmium ion | Cd | 5 |
Water and common crystallization additives (K, NA, CL) are not listed.
Primary citation
Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction. Schmeing, T.M., Huang, K.S., Kitchen, D.E. et al. Mol Cell (2005) 20:437-448. DOI 10.1016/j.molcel.2005.09.006 · PubMed
Other PDB entries of the same protein (UniProt P20276 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1VQ8 2.2 Å, The structure of CCDA-PHE-CAP-BIO and the antibiotic sparsomycin bound to the large…
- 1VQO 2.2 Å, The structure of CCPMN bound to the large ribosomal subunit haloarcula marismortui
- 1VQP 2.25 Å, The structure of the transition state analogue "RAP" bound to the large ribosomal…
- 1VQK 2.3 Å, The structure of CCDA-PHE-CAP-BIO bound to the a site of the ribosomal subunit of…
- 1VQL 2.3 Å, The structure of the transition state analogue "DCSN" bound to the large ribosomal…
- 1VQM 2.3 Å, The structure of the transition state analogue "DAN" bound to the large ribosomal…
- 1FFK 2.4 Å, Crystal structure of the large ribosomal subunit from haloarcula marismortui at 2.4 Å…
- 1JJ2 2.4 Å, Fully Refined Crystal Structure of the Haloarcula marismortui Large Ribosomal Subunit at…
- 1S72 2.4 Å, Refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 Å…
- 1VQN 2.4 Å, The structure of CC-HPMN AND CCA-PHE-CAP-BIO bound to the large ribosomal subunit of…
- 1YHQ 2.4 Å, Crystal Structure Of Azithromycin Bound To The G2099A Mutant 50S Ribosomal Subunit Of…
- 3CC2 2.4 Å, The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at…
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