PDB-6ig1: DNA polymerase IV - DNA ternary complex 10

ID or keywords:

Entry

Database: PDB / ID: 6ig1

Title

DNA polymerase IV - DNA ternary complex 10

Components

DNA polymerase IV
DTN3

Keywords

DNA BINDING PROTEIN / DNA POLYMERASE / 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: 1.97 Å

Authors

Kottur, J. / Nair, D.T.

Funding support

India, 1items

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	Sep 21, 2018	Deposition site: PDBJ / Processing site: PDBJ
Supersession	Nov 28, 2018	ID: 5YV4
Revision 1.0	Nov 28, 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 / struct_conn_type 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_alt_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.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_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ig1.cif.gz	367.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6ig1.ent.gz	292.6 KB	Display	PDB format
PDBx/mmJSON format	6ig1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ig1_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6ig1_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6ig1_validation.xml.gz	35.3 KB	Display
Data in CIF	6ig1_validation.cif.gz	51.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ig/6ig1 ftp://data.pdbj.org/pub/pdb/validation_reports/ig/6ig1	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 5zlvC 4ir1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5yv3-1 5yye-1 2c2d-d 4irc-1 5yyd-1 5yv0-1 4irk-1 4irk-2 4ir1-1 5yv2-1 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

Related items in Molecule of the Month

#67 - Jul 2005
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similarity (1)
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Zinc Fingers
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similarity (1)
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similarity (1)
#160 - Apr 2013
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similarity (1)
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similarity (1)
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similarity (1)
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similarity (1)
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Deposited unit

F: DNA polymerase IV

A: DNA polymerase IV

G: DTN3

H: DTN3

B: DTN3

C: DTN3

hetero molecules

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

1

F: DNA polymerase IV

G: DTN3

H: DTN3

hetero molecules

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

2

A: DNA polymerase IV

B: DTN3

C: DTN3

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.380, 57.160, 110.580
Angle α, β, γ (deg.)	90.00, 94.49, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein / DNA chain , 2 types, 6 molecules FAGHBC

#1: Protein	DNA polymerase IV / Pol IV / Translesion synthesis polymerase IV / TSL polymerase IV Mass: 39589.895 Da / Num. of mol.: 2 / Fragment: UNP residues 2-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: dinB, dinP, b0231, JW0221 / Production host: Escherichia coli (E. coli) / References: UniProt: Q47155, DNA-directed DNA polymerase
#2: DNA chain	DTN3 Mass: 5796.747 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria)

#1: Protein

DNA polymerase IV / Pol IV / Translesion synthesis polymerase IV / TSL polymerase IV

Mass: 39589.895 Da / Num. of mol.: 2 / Fragment: UNP residues 2-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: dinB, dinP, b0231, JW0221 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q47155, DNA-directed DNA polymerase

#2: DNA chain

DTN3

Mass: 5796.747 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.)

Escherichia coli K-12 (bacteria)

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Non-polymers , 4 types, 484 molecules

#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-DPO / DIPHOSPHATE Mass: 173.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O₇P₂
#5: Chemical	ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₂O₁₄P₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 476 / 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 %
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
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 21, 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: 1.97→55.12 Å / Num. obs: 76471 / % possible obs: 99.7 % / Redundancy: 4.8 % / R_merge(I) obs: 0.063 / Net I/σ(I): 12.9
Reflection shell	Resolution: 1.97→2.08 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.644 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 11032 / % possible all: 99.6

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4IR1

4ir1

Resolution: 1.97→44.86 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 28.46

	R_factor	Num. reflection	% reflection
R_free	0.243	7476	5.05 %
R_work	0.201	-	-
obs	0.203	76227	99.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.97→44.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5374	1363	80	476	7293

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7092
X-RAY DIFFRACTION	f_angle_d	1.072	9880
X-RAY DIFFRACTION	f_dihedral_angle_d	22.589	4140
X-RAY DIFFRACTION	f_chiral_restr	0.058	1095
X-RAY DIFFRACTION	f_plane_restr	0.007	1033

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 (%)
1.97-1.9924	0.3853	254	0.3303	4637	X-RAY DIFFRACTION	99
1.9924-2.0158	0.3798	240	0.3103	4698	X-RAY DIFFRACTION	99
2.0158-2.0404	0.3335	212	0.2979	4756	X-RAY DIFFRACTION	98
2.0404-2.0662	0.3356	227	0.3006	4592	X-RAY DIFFRACTION	99
2.0662-2.0934	0.3051	242	0.3031	4660	X-RAY DIFFRACTION	99
2.0934-2.1221	0.3246	242	0.2742	4709	X-RAY DIFFRACTION	98
2.1221-2.1524	0.3101	285	0.2588	4637	X-RAY DIFFRACTION	100
2.1524-2.1845	0.2769	243	0.2492	4691	X-RAY DIFFRACTION	99
2.1845-2.2187	0.3318	268	0.2578	4618	X-RAY DIFFRACTION	99
2.2187-2.2551	0.3052	252	0.2736	4715	X-RAY DIFFRACTION	99
2.2551-2.2939	0.2899	217	0.2525	4701	X-RAY DIFFRACTION	99
2.2939-2.3357	0.3306	256	0.2397	4678	X-RAY DIFFRACTION	100
2.3357-2.3806	0.2874	261	0.2408	4682	X-RAY DIFFRACTION	99
2.3806-2.4292	0.3073	282	0.2397	4620	X-RAY DIFFRACTION	100
2.4292-2.482	0.2639	241	0.2381	4752	X-RAY DIFFRACTION	99
2.482-2.5397	0.2746	251	0.2285	4680	X-RAY DIFFRACTION	100
2.5397-2.6032	0.2663	266	0.2276	4723	X-RAY DIFFRACTION	99
2.6032-2.6736	0.3221	237	0.2337	4623	X-RAY DIFFRACTION	100
2.6736-2.7523	0.2818	264	0.2209	4741	X-RAY DIFFRACTION	100
2.7523-2.8411	0.2569	295	0.2159	4673	X-RAY DIFFRACTION	100
2.8411-2.9426	0.2421	228	0.2174	4707	X-RAY DIFFRACTION	100
2.9426-3.0604	0.2795	222	0.2211	4730	X-RAY DIFFRACTION	100
3.0604-3.1996	0.2675	249	0.2085	4745	X-RAY DIFFRACTION	100
3.1996-3.3683	0.2127	218	0.1866	4793	X-RAY DIFFRACTION	100
3.3683-3.5792	0.2017	237	0.1801	4743	X-RAY DIFFRACTION	100
3.5792-3.8554	0.2197	262	0.1766	4658	X-RAY DIFFRACTION	100
3.8554-4.2432	0.2472	240	0.1606	4696	X-RAY DIFFRACTION	100
4.2432-4.8565	0.2043	243	0.1548	4740	X-RAY DIFFRACTION	100
4.8565-6.1163	0.2046	264	0.166	4722	X-RAY DIFFRACTION	100
6.1163-44.8691	0.1557	278	0.1568	4517	X-RAY DIFFRACTION	97

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	0.0969	-0.0262	0.0881	0.1326	-0.0058	0.1919	-0.072	0.0275	0.015	-0.2462	0.0462	-0.6858	0.0613	-0.0337	-0.0005	0.154	-0.0258	0.0733	0.1651	-0.0253	0.5034	4.6142	-14.0598	-70.211
2	0.0354	-0.0084	0.0776	0.076	0.015	0.1319	-0.1522	0.0007	0.4774	-0.1323	-0.1646	0.1625	-0.1657	-0.1436	-0.0109	0.2343	0.0153	-0.0958	0.1775	-0.0195	0.5229	-12.7109	3.1827	-69.5279
3	0.0795	-0.0714	0.0472	0.0303	-0.0302	0.0765	-0.2815	-0.1297	0.0728	0.3249	0.0281	-0.3023	-0.0846	0.0061	-0.001	0.2559	0.049	-0.1195	0.2104	-0.0686	0.5159	1.1964	-14.8158	-44.6312
4	0.7705	0.1675	-0.0919	0.492	-0.573	0.9869	-0.183	-0.2936	0.6459	-0.3937	0.2787	0.089	0.5736	-0.4759	0.2127	0.0097	-0.0235	0.1058	0.4136	-0.2326	0.2245	-30.8721	-19.0656	-64.3598
5	0.0387	0.029	0.013	0.0635	-0.0246	0.059	0.08	-0.0708	-0.152	0.2341	-0.0021	-0.1847	0.223	0.2462	-0.0001	0.5504	0.0863	-0.0932	0.3989	-0.0043	0.2459	-28.0339	-8.3162	3.1999
6	0.0246	0.0321	-0.0457	0.0574	-0.0167	0.029	0.1551	-0.0134	0.0894	-0.0288	0.0435	-0.1518	-0.4353	0.4083	-0	0.589	-0.0367	0.0128	0.377	-0.0578	0.276	-25.7636	8.5704	-14.6806
7	0.0573	-0.009	0.0044	0.0287	-0.0125	0.0283	0.0739	-0.0872	0.0581	0.0265	0.0278	0.2441	0.1208	-0.3075	-0.0001	0.5254	-0.0114	0.0457	0.4125	0.0195	0.237	-52.7449	-9.099	-4.4882
8	0.0986	-0.0131	-0.0866	0.1272	0.1592	0.2254	-0.0458	0.1244	-0.0782	0.0817	-0.0458	-0.071	0.1252	0.2191	-0.0015	0.3744	0.1354	0.0157	0.3479	-0.0066	0.169	-27.9013	-15.0345	-32.5987
9	0.4798	-0.1053	0.3114	0.1757	0.0817	0.2485	-0.1185	-0.1546	-0.0767	-0.1041	-0.0452	-0.1722	0.0396	-0.1097	-0.0664	0.1441	0.0033	0.0611	0.2593	-0.0321	0.3193	-17.9379	-22.6444	-54.2655
10	0.0838	-0.0054	-0.002	0.0756	-0.0461	0.0374	0.0913	-0.125	-0.0223	0.071	-0.0977	-0.0288	-0.0067	-0.1217	-0	0.4771	-0.0094	-0.0179	0.3254	-0.0452	0.1801	-41.5773	-19.0417	-22.8521

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'F' AND (RESID 0 THROUGH 10 OR RESID 76 THROUGH 164 )
2	X-RAY DIFFRACTION	2	CHAIN 'F' AND (RESID 11 THROUGH 75 )
3	X-RAY DIFFRACTION	3	CHAIN 'F' AND (RESID 165 THROUGH 229 )
4	X-RAY DIFFRACTION	4	CHAIN 'F' AND (RESID 241 THROUGH 341 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 0 THROUGH 10 OR RESID 76 THROUGH 164 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 11 THROUGH 75 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 165 THROUGH 229 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 241 THROUGH 341 )
9	X-RAY DIFFRACTION	9	CHAIN 'H' AND (RESID 861 THROUGH 874 OR RESID 901) OR CHAIN 'G' AND (RESID 838 THROUGH 854) OR CHAIN 'F' AND (RESID 901 THROUGH 903)
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 838 THROUGH 854 OR RESID 901) OR CHAIN 'C' AND (RESID 858 THROUGH 874) OR CHAIN 'A' AND (RESID 901 THROUGH 903)

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+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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Validation report

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Assembly

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Components

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Protein / DNA chain , 2 types, 6 molecules FAGHBC

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Non-polymers , 4 types, 484 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi