1PRC: Crystallographic refinement

Name: PDB 1PRC: Crystallographic refinement at 2.3 Å resolution and refined model of the photosynthetic reaction center from rhodopseudomonas viridis
Published: 1989-01-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: photosynthetic reaction center

Crystallographic refinement at 2.3 Å resolution and refined model of the photosynthetic reaction center from rhodopseudomonas viridis. Determined by X-ray diffraction at 2.3 Å resolution. Released 9 Jan 1989.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Blastochloris viridis
Chains: 4
Atoms: 10,288
Mol. weight: 142.93 kDa
Ligands: HEC, BCB, BPB, UQ1
Released: 9 Jan 1989

Explore 1PRC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1PRC contains 81 α-helices and 46 β-strands across 4 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 C: 27 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	8-9	2	1
β-strand	22-23	2	1
α-helix	25-34	10
α-helix	35-37	3
α-helix	39-44	6
α-helix	52-55	4
α-helix	67-81	15
α-helix	87-89	3
α-helix	102-120	19
α-helix	122-125	4
α-helix	132-136	5
β-strand	146	1	2
α-helix	159-161	3
α-helix	169-171	3
α-helix	172-177	6
α-helix	189	1
α-helix	190-194	5
β-strand	211	1	3
α-helix	217-219	3
α-helix	221-222	2
α-helix	224-239	16
α-helix	244-247	4
β-strand	248	1	4
β-strand	257	1	5
β-strand	260	1	4
α-helix	262-277	16
α-helix	278-282	5
α-helix	283-286	4
α-helix	291-293	3
α-helix	299-301	3
β-strand	302	1	2
α-helix	305-309	5
α-helix	315-318	4
α-helix	326-328	3

Chain H: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	3
β-strand	5-7	3	16
β-strand	10-11	2	16
α-helix	12-25	14
α-helix	26-32	7
α-helix	33-35	3
β-strand	44	1	6
α-helix	56-60	5
β-strand	66-69	4	17
α-helix	70	1
β-strand	75-78	4	17
β-strand	90-92	3	7
β-strand	101-103	3	7
α-helix	107-110	4
α-helix	113-115	3
β-strand	124	1	18
β-strand	126	1	19
β-strand	132	1	19
β-strand	134-136	3	20
β-strand	144-145	2	11
α-helix	146	1
α-helix	155	1
β-strand	156-158	3	20
β-strand	164-174	11	20
β-strand	179-187	9	20
β-strand	193-197	5	20
α-helix	198-200	3
β-strand	202-203	2	20
β-strand	208-209	2	20
α-helix	215-218	4
α-helix	222-224	3
β-strand	231	1	18
α-helix	232-248	17

Chain L: 18 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	6
α-helix	7-9	3
β-strand	11	1	7
α-helix	19-21	3
β-strand	25-26	2	8
β-strand	29-30	2	8
α-helix	33-53	21
β-strand	65-66	2	9
α-helix	71-73	3
α-helix	80-82	3
α-helix	84-111	28
α-helix	116-129	14
α-helix	130-134	5
α-helix	135-139	5
α-helix	142-144	3
β-strand	148-149	2	9
α-helix	152-162	11
α-helix	167-169	3
α-helix	171-198	28
α-helix	204-206	3
α-helix	209-220	12
α-helix	226-249	24
β-strand	251	1	10
β-strand	255	1	10
α-helix	259-262	4
α-helix	264-267	4

Chain M: 23 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	12-13	2	11
α-helix	25-27	3
β-strand	28-29	2	12
β-strand	33-34	2	13
α-helix	38-40	3
β-strand	45-46	2	13
β-strand	49-50	2	12
α-helix	52-76	25
α-helix	81-87	7
α-helix	88-90	3
β-strand	93	1	14
α-helix	94-96	3
α-helix	107-111	5
α-helix	112-137	26
α-helix	143-156	14
α-helix	157-161	5
α-helix	162-166	5
α-helix	169-171	3
β-strand	175	1	14
α-helix	179-190	12
α-helix	194-196	3
α-helix	198-223	26
α-helix	225-227	3
α-helix	232-237	6
α-helix	241-254	14
α-helix	260-284	25
β-strand	285	1	15
β-strand	289	1	15
α-helix	292-298	7
α-helix	310-311	2
β-strand	312	1	5
α-helix	315-317	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Photosynthetic reaction center	C	protein	336	Blastochloris viridis	P07173 (AlphaFold model)
Photosynthetic reaction center	L	protein	273	Blastochloris viridis	P06009 (AlphaFold model)
Photosynthetic reaction center	M	protein	323	Blastochloris viridis	P06010 (AlphaFold model)
Photosynthetic reaction center	H	protein	258	Blastochloris viridis	P06008 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>1PRC_1 PHOTOSYNTHETIC REACTION CENTER (chains C)
CFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVK
VLGNLTEAEFLRTMTAITEWVSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTN
WTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETPTHVERVETRSGYVVRLAKYT
AYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSL
GTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEA
PQADCRTCHQGVTKPLFGASRLKDYPELGPIKAAAK

Sequence of entity 2 (L), FASTA

>1PRC_2 PHOTOSYNTHETIC REACTION CENTER (chains L)
ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWD
PFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLA
FCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFL
FVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNI
FLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS

Sequence of entity 3 (M), FASTA

>1PRC_3 PHOTOSYNTHETIC REACTION CENTER (chains M)
ADYQTIYTQIQARGPHITVSGEWGDNDRVGKPFYSYWLGKIGDAQIGPIYLGASGIAAFA
FGSTAILIILFNMAAEVHFDPLQFFRQFFWLGLYPPKAQYGMGIPPLHDGGWWLMAGLFM
TLSLGSWWIRVYSRARALGLGTHIAWNFAAAIFFVLCIGCIHPTLVGSWSEGVPFGIWPH
IDWLTAFSIRYGNFYYCPWHGFSIGFAYGCGLLFAAHGATILAVARFGGDREIEQITDRG
TAVERAALFWRWTIGFNATIESVHRWGWFFSLMVMVSASVGILLTGTFVDNWYLWCVKHG
AAPDYPAYLPATPDPASLPGAPK

Sequence of entity 4 (H), FASTA

>1PRC_4 PHOTOSYNTHETIC REACTION CENTER (chains H)
MYHGALAQHLDIAQLVWYAQWLVIWTVVLLYLRREDRREGYPLVEPLGLVKLAPEDGQVY
ELPYPKTFVLPHGGTVTVPRRRPETRELKLAQTDGFEGAPLQPTGNPLVDAVGPASYAER
AEVVDATVDGKAKIVPLRVATDFSIAEGDVDPRGLPVVAADGVEAGTVTDLWVDRSEHYF
RYLELSVAGSARTALIPLGFCDVKKDKIVVTSILSEQFANVPRLQSRDQITLREEDKVSA
YYAGGLLYATPERAESLL

Ligands and cofactors

ID	Name	Formula	Copies
HEC	Heme C	C34 H36 Fe N4 O4	4
BCB	Bacteriochlorophyll B	C55 H72 Mg N4 O6	4
BPB	Bacteriopheophytin B	C55 H74 N4 O6	2
UQ1	Ubiquinone-1	C14 H18 O4	1
FE	FE (III) ion	Fe	1
MQ7	Menaquinone-7	C46 H64 O2	1
NS1	15-trans-1,2-dihydroneurosporene	C40 H60	1
LDA	Lauryl dimethylamine-N-oxide	C14 H31 N O	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Crystallographic refinement at 2.3 A resolution and refined model of the photosynthetic reaction centre from Rhodopseudomonas viridis. Deisenhofer, J., Epp, O., Sinning, I. et al. J Mol Biol (1995) 246:429-457. DOI 10.1006/jmbi.1994.0097 · PubMed

Other PDB entries of the same protein (UniProt P07173 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2WJN 1.86 Å, Lipidic sponge phase crystal structure of photosynthetic reaction centre from…
3T6E 1.92 Å, Crystal Structure of the Reaction Centre from Blastochloris viridis strain DSM 133 (ATCC…
2WJM 1.95 Å, Lipidic sponge phase crystal structure of the photosynthetic reaction centre from…
3T6D 1.95 Å, Crystal Structure of the Reaction Centre from Blastochloris viridis strain DSM 133 (ATCC…
2I5N 1.96 Å, 1.96 A X-ray structure of photosynthetic reaction center from Rhodopseudomonas…
1DXR 2.0 Å, Photosynthetic reaction center from Rhodopseudomonas viridis - His L168 Phe mutant…
1VRN 2.2 Å, Photosynthetic reaction center blastochloris viridis (ATCC)
7Q7Q 2.25 Å, Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic…
6PRC 2.3 Å, Photosynthetic reaction center from rhodopseudomonas viridis (dg-420314 (triazine)…
5PRC 2.35 Å, Photosynthetic reaction center from rhodopseudomonas viridis (atrazine complex)
2JBL 2.4 Å, Photosynthetic reaction center from blastochloris viridis
3PRC 2.4 Å, Photosynthetic reaction center from rhodopseudomonas viridis (qb-depleted)

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1PRC is part of these collections:

Photosynthesis

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