PDB-5zlv: DNA polymerase IV - DNA ternary complex with 50mM MgCl2

ID or keywords:

Entry

Database: PDB / ID: 5zlv

Title

DNA polymerase IV - DNA ternary complex with 50mM MgCl2

Components

DNA polymerase IV
DTN1
DTN2

Keywords

DNA BINDING PROTEIN/DNA / DNA POLYMERASE / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

SOS response / error-free translesion synthesis / DNA synthesis involved in DNA repair / error-prone translesion synthesis / DNA-templated DNA replication / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA damage response / magnesium ion binding / cytoplasm
Similarity search - Function

Biological species

Escherichia coli K-12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Kottur, J. / Nair, D.T.

Citation

Journal: Nucleic Acids Res. / Year: 2018
Title: Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction
Authors: Kottur, J. / Nair, D.T.

History

Deposition	Mar 29, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 7, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5zlv.cif.gz	359.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5zlv.ent.gz	286 KB	Display	PDB format
PDBx/mmJSON format	5zlv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5zlv_validation.pdf.gz	490.5 KB	Display	wwPDB validaton report
Full document	5zlv_full_validation.pdf.gz	500.9 KB	Display
Data in XML	5zlv_validation.xml.gz	33.1 KB	Display
Data in CIF	5zlv_validation.cif.gz	48.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zl/5zlv ftp://data.pdbj.org/pub/pdb/validation_reports/zl/5zlv	HTTPS FTP

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Related structure data

Related structure data	5yurC 5yusC 5yutC 5yuuC 5yuvC 5yuwC 5yuxC 5yuyC 5yuzC 5yv0C 5yv1C 5yv2C 5yv3C 5yydC 5yyeC 6ig1C 4ir1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6vg6-1 5yv0-1 5yyd-1 4q45-1 5yuw-2 6ig1-1 2agp-1 3gil-2 2c2r-d 4qwb-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

F: DNA polymerase IV

A: DNA polymerase IV

G: DTN2

H: DTN1

B: DTN2

C: DTN1

hetero molecules

102 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

F: DNA polymerase IV

G: DTN2

H: DTN1

hetero molecules

defined by author&software
51.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: DNA polymerase IV

B: DTN2

C: DTN1

hetero molecules

defined by author&software
51.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.310, 57.240, 110.390
Angle α, β, γ (deg.)	90.00, 94.74, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules FA

#1: Protein	DNA polymerase IV / Pol IV / Translesion synthesis polymerase IV / TSL polymerase IV Mass: 39589.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q47155, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules GBHC

#2: DNA chain	DTN2 Mass: 5492.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria)
#3: DNA chain	DTN1 Mass: 5796.747 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria)

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Non-polymers , 4 types, 452 molecules

#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#6: Chemical	ChemComp-DPO / DIPHOSPHATE Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O₇P₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.67 Å³/Da / Density % sol: 53.94 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 15% MPD , pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 20, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95372 Å / Relative weight: 1
Reflection	Resolution: 2.35→65.2 Å / Num. obs: 45186 / % possible obs: 98.4 % / Redundancy: 3.6 % / CC_1/2: 0.995 / Net I/σ(I): 9.3
Reflection shell	Resolution: 2.35→2.48 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 6322 / CC_1/2: 0.736 / % possible all: 96.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4IR1

4ir1

Resolution: 2.35→50.778 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 27.47

	R_factor	Num. reflection	% reflection
R_free	0.2485	4305	5.08 %
R_work	0.1884	-	-
obs	0.1915	44410	96.71 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.35→50.778 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5382	1308	24	444	7158

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6962
X-RAY DIFFRACTION	f_angle_d	1.009	9677
X-RAY DIFFRACTION	f_dihedral_angle_d	19.799	3997
X-RAY DIFFRACTION	f_chiral_restr	0.055	1088
X-RAY DIFFRACTION	f_plane_restr	0.006	1026

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.35-2.3767	0.3374	149	0.2734	2557	X-RAY DIFFRACTION	94
2.3767-2.4047	0.4064	160	0.2871	2544	X-RAY DIFFRACTION	92
2.4047-2.434	0.3241	135	0.2906	2589	X-RAY DIFFRACTION	94
2.434-2.4648	0.3329	154	0.2826	2563	X-RAY DIFFRACTION	93
2.4648-2.4972	0.3537	136	0.2812	2625	X-RAY DIFFRACTION	95
2.4972-2.5314	0.3395	125	0.264	2644	X-RAY DIFFRACTION	93
2.5314-2.5676	0.3663	143	0.2699	2635	X-RAY DIFFRACTION	95
2.5676-2.6059	0.3153	154	0.2709	2632	X-RAY DIFFRACTION	94
2.6059-2.6466	0.3574	126	0.2671	2582	X-RAY DIFFRACTION	94
2.6466-2.69	0.3675	146	0.2608	2600	X-RAY DIFFRACTION	94
2.69-2.7364	0.3193	157	0.2454	2666	X-RAY DIFFRACTION	95
2.7364-2.7862	0.2722	142	0.2284	2609	X-RAY DIFFRACTION	95
2.7862-2.8398	0.2976	175	0.2277	2619	X-RAY DIFFRACTION	96
2.8398-2.8977	0.2956	123	0.2287	2693	X-RAY DIFFRACTION	95
2.8977-2.9607	0.3406	122	0.2268	2673	X-RAY DIFFRACTION	96
2.9607-3.0296	0.3253	124	0.231	2679	X-RAY DIFFRACTION	97
3.0296-3.1053	0.3043	139	0.2107	2670	X-RAY DIFFRACTION	97
3.1053-3.1893	0.2787	151	0.1884	2762	X-RAY DIFFRACTION	97
3.1893-3.2831	0.2836	120	0.1801	2672	X-RAY DIFFRACTION	98
3.2831-3.3891	0.2156	122	0.1743	2798	X-RAY DIFFRACTION	99
3.3891-3.5102	0.2053	141	0.1673	2711	X-RAY DIFFRACTION	99
3.5102-3.6507	0.2408	150	0.1768	2792	X-RAY DIFFRACTION	99
3.6507-3.8168	0.2171	149	0.1576	2791	X-RAY DIFFRACTION	100
3.8168-4.0179	0.2157	172	0.1587	2746	X-RAY DIFFRACTION	100
4.0179-4.2695	0.2094	108	0.14	2800	X-RAY DIFFRACTION	100
4.2695-4.599	0.206	155	0.1348	2759	X-RAY DIFFRACTION	100
4.599-5.0614	0.21	150	0.1424	2783	X-RAY DIFFRACTION	100
5.0614-5.7929	0.2034	158	0.1556	2787	X-RAY DIFFRACTION	100
5.7929-7.295	0.2084	165	0.1737	2748	X-RAY DIFFRACTION	100
7.295-50.7898	0.1388	154	0.1499	2753	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.998	-0.1278	0.7077	1.1166	-0.1871	1.6413	-0.0292	0.2067	-0.0055	-0.3543	-0.0197	-0.5933	0.0237	0.0488	0.0199	0.1843	-0.0167	0.0694	0.1801	-0.0078	0.3827	4.9559	-14.2921	-70.1497
2	0.5725	-0.1487	0.583	1.977	0.0212	0.7734	-0.0587	0.1123	0.4059	-0.1997	-0.2008	0.0005	-0.1339	-0.0851	0.1503	0.2085	0.0143	-0.0903	0.2012	0.0244	0.4445	-12.4278	3.0736	-69.4036
3	1.2634	-0.245	0.3157	1.1342	0.0163	0.9094	-0.2058	-0.2874	0.0191	0.4403	-0.0408	-0.1292	-0.0664	-0.1075	0.1652	0.2575	0.0371	-0.1009	0.2289	-0.0713	0.4793	1.4484	-14.8518	-44.4422
4	2.0119	0.2879	0.432	2.0471	-0.2653	1.2981	-0.0928	-0.2245	0.311	-0.1113	0.1558	0.2427	0.1617	-0.3598	-0.0124	0.0715	-0.0393	0.0128	0.3222	-0.0936	0.1976	-30.5647	-19.1892	-64.1762
5	1.3296	0.1017	0.1403	1.1634	0.0966	0.8619	0.0535	-0.0632	-0.1299	0.2427	-0.0704	-0.2597	0.2947	0.1877	-0.02	0.4507	0.0612	-0.0567	0.3077	0.0156	0.2312	-28.0687	-8.4113	3.2789
6	0.7991	0.0091	-0.4715	1.4574	0.1054	1.0203	0.2297	0.0725	0.0242	-0.0285	-0.0319	-0.2789	-0.4678	0.2668	-0.1652	0.5488	-0.04	0.0048	0.3043	-0.0287	0.2852	-25.5988	8.5093	-14.5929
7	0.8276	-0.1103	-0.0572	1.0175	-0.3351	0.9461	-0.0148	-0.0065	-0.0055	-0.0364	0.0444	0.2842	-0.0254	-0.255	-0.0333	0.4525	-0.0045	0.0135	0.3099	0.0028	0.2126	-52.872	-9.0758	-4.5173
8	1.1394	0.0125	-0.0084	1.5985	0.1534	1.9426	-0.1069	0.1069	-0.1924	0.1681	-0.0659	-0.0567	0.0835	0.2117	0.1412	0.3558	0.1009	0.044	0.3192	-0.0052	0.2317	-27.7164	-15.134	-32.5334
9	2.195	0.4835	0.0071	1.6739	-0.7307	1.6522	-0.0957	-0.4159	-0.205	0.1159	-0.1139	-0.0294	0.0493	-0.2485	0.1133	0.1474	-0.0196	0.0587	0.2666	-0.0028	0.2632	-18.3029	-23.0881	-53.6577
10	0.7963	0.8148	0.4713	1.3707	0.6608	0.6585	0.1164	0.0113	0.0107	0.0025	-0.1901	0.0428	0.0487	-0.2081	0.029	0.4855	0.0049	0.0137	0.3729	-0.0405	0.2504	-42.181	-20.2816	-23.7799

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN F AND ( RESID 0:10 OR RESID 76:164 ) )	F	0 - 10
2	X-RAY DIFFRACTION	1	( CHAIN F AND ( RESID 0:10 OR RESID 76:164 ) )	F	76 - 164
3	X-RAY DIFFRACTION	2	( CHAIN F AND RESID 11:75 )	F	11 - 75
4	X-RAY DIFFRACTION	3	( CHAIN F AND RESID 165:229 )	F	165 - 229
5	X-RAY DIFFRACTION	4	( CHAIN F AND RESID 241:341 )	F	241 - 341
6	X-RAY DIFFRACTION	5	( CHAIN A AND ( RESID 0:10 OR RESID 76:164 ) )	A	0 - 10
7	X-RAY DIFFRACTION	5	( CHAIN A AND ( RESID 0:10 OR RESID 76:164 ) )	A	76 - 164
8	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 11:75 )	A	11 - 75
9	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 165:229 )	A	165 - 229
10	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 241:341 )	A	241 - 341
11	X-RAY DIFFRACTION	9	( CHAIN H AND ( RESID 861:874 OR RESID 901:901 ) ) OR ( CHAIN G AND RESID 838:853 ) OR ( CHAIN F AND RESID 901:904 )	H	861 - 874
12	X-RAY DIFFRACTION	9	( CHAIN H AND ( RESID 861:874 OR RESID 901:901 ) ) OR ( CHAIN G AND RESID 838:853 ) OR ( CHAIN F AND RESID 901:904 )	H	901
13	X-RAY DIFFRACTION	9	( CHAIN H AND ( RESID 861:874 OR RESID 901:901 ) ) OR ( CHAIN G AND RESID 838:853 ) OR ( CHAIN F AND RESID 901:904 )	G	838 - 853
14	X-RAY DIFFRACTION	9	( CHAIN H AND ( RESID 861:874 OR RESID 901:901 ) ) OR ( CHAIN G AND RESID 838:853 ) OR ( CHAIN F AND RESID 901:904 )	F	901 - 904
15	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 901:903 ) OR ( CHAIN C AND RESID 858:874 ) OR ( CHAIN B AND RESID 838:854 )	A	901 - 903
16	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 901:903 ) OR ( CHAIN C AND RESID 858:874 ) OR ( CHAIN B AND RESID 838:854 )	C	858 - 874
17	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 901:903 ) OR ( CHAIN C AND RESID 858:874 ) OR ( CHAIN B AND RESID 838:854 )	B	838 - 854

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Protein , 1 types, 2 molecules FA

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DNA chain , 2 types, 4 molecules GBHC

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Protein , 1 types, 2 molecules FA

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DNA chain , 2 types, 4 molecules GBHC

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Non-polymers , 4 types, 452 molecules

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Experimental details

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Experiment

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