4R8U: S-SAD structure of DINB-DNA Complex

S-SAD structure of DINB-DNA Complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 14 Jan 2015.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Escherichia coli K-12, synthetic construct
Chains: 6
Atoms: 6,841
Mol. weight: 98.11 kDa
Ligands: 1FZ, MG
Released: 14 Jan 2015

Explore 4R8U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4R8U contains 37 α-helices and 36 β-strands across 2 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 A: 18 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	1
α-helix	13-21	9
α-helix	23-25	3
β-strand	30-33	4	2
β-strand	41	1	3
β-strand	42-45	4	2
α-helix	47-50	4
β-strand	59	1	3
α-helix	60-66	7
α-helix	70	1
β-strand	71-73	3	2
α-helix	77-92	16
β-strand	98-102	5	1
β-strand	105-109	5	1
α-helix	116-118	3
α-helix	120-135	16
β-strand	139-144	6	1
α-helix	147-156	10
β-strand	162-164	3	1
α-helix	167-169	3
α-helix	170-175	6
β-strand	178	1	4
α-helix	179-181	3
α-helix	187-194	8
β-strand	200	1	4
α-helix	201-205	5
α-helix	209-216	8
α-helix	218-227	10
β-strand	243-254	12	5
α-helix	257-278	22
β-strand	283	1	6
β-strand	286-293	8	5
β-strand	298-304	7	5
β-strand	307	1	6
α-helix	310-324	15
β-strand	330-338	9	5

Chain B: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	7
α-helix	13-21	9
α-helix	23-25	3
β-strand	30-33	4	8
α-helix	36-38	3
β-strand	41	1	9
β-strand	42-45	4	8
α-helix	47-50	4
β-strand	59	1	9
α-helix	60-66	7
β-strand	71-73	3	8
α-helix	77-94	18
β-strand	98-102	5	7
β-strand	105-109	5	7
α-helix	115-118	4
α-helix	120-135	16
β-strand	139-144	6	7
α-helix	147-154	8
β-strand	162-164	3	7
α-helix	167-169	3
α-helix	170-175	6
β-strand	178	1	10
α-helix	179-181	3
α-helix	187-194	8
β-strand	200	1	10
α-helix	201-205	5
α-helix	209-216	8
α-helix	218-227	10
α-helix	233-235	3
β-strand	243-254	12	11
α-helix	257-276	20
β-strand	283	1	12
β-strand	286-293	8	11
β-strand	298-304	7	11
β-strand	307	1	12
α-helix	310-324	15
β-strand	330-338	9	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase IV	A	protein	340	Escherichia coli K-12	Q47155 (AlphaFold model)
DNA polymerase IV	B	protein	338	Escherichia coli K-12	Q47155 (AlphaFold model)
DNA	C, V	DNA	17	synthetic construct
DNA	W	DNA	18	synthetic construct
DNA	D	DNA	16	synthetic construct

Sequence of entity 1 (A), FASTA

>4R8U_1 DNA polymerase IV (chains A)
SRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTG
MALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSAT
LIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAK
IPGVGKVSAAKLEAMGLRTCGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLR
KSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQ
EHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLD

Sequence of entity 2 (B), FASTA

>4R8U_2 DNA polymerase IV (chains B)
RKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGM
ALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATL
IAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKI
PGVGKVSAAKLEAMGLRTCGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRK
SVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQE
HVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLD

Sequence of entity 3 (C, V), FASTA

>4R8U_3 DNA (chains C, V)
CTAGGGTCCTAGGACCC

Sequence of entity 4 (W), FASTA

>4R8U_4 DNA (chains W)
TCTAGGGTCCTAGGACCC

Sequence of entity 5 (D), FASTA

>4R8U_5 DNA (chains D)
TAGGGTCCTAGGACCC

Ligands and cofactors

ID	Name	Formula	Copies
1FZ	5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidi…	C10 H18 N3 O13 P3	2
MG	Magnesium ion	Mg	2

Primary citation

Fast native-SAD phasing for routine macromolecular structure determination. Weinert, T., Olieric, V., Waltersperger, S. et al. Nat Methods (2015) 12:131-133. DOI 10.1038/nmeth.3211 · PubMed

Other PDB entries of the same protein (UniProt Q47155 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1OK7 1.65 Å, A Conserved protein binding-site on Bacterial Sliding Clamps
5YUY 1.74 Å, DNA polymerase IV - DNA ternary complex 9
5YUZ 1.83 Å, DNA polymerase IV - DNA ternary complex 11
5YUU 1.89 Å, DNA polymerase IV - DNA ternary complex 4
1UNN 1.9 Å, Complex of beta-clamp processivity factor and little finger domain of PolIV
5YV2 1.9 Å, DNA polymerase IV - DNA ternary complex 14
5YUS 1.94 Å, DNA polymerase IV - DNA ternary complex 2
6IG1 1.97 Å, DNA polymerase IV - DNA ternary complex 10
5YV3 2.03 Å, DNA polymerase IV - DNA ternary complex 7
5YUR 2.04 Å, DNA polymerase IV - DNA ternary complex 1
5YUX 2.04 Å, DNA polymerase IV - DNA ternary complex 8
5YYD 2.05 Å, DNA polymerase IV - ternary complex 15

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