PDB-5yv3: DNA polymerase IV - DNA ternary complex 7

ID or keywords:

Entry

Database: PDB / ID: 5yv3

Title

DNA polymerase IV - DNA ternary complex 7

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

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

Biological species

Escherichia coli K-12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.03 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	Nov 23, 2017	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 / 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.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_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

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Validation report

Summary document	5yv3_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	5yv3_full_validation.pdf.gz	1.2 MB	Display
Data in XML	5yv3_validation.xml.gz	34.5 KB	Display
Data in CIF	5yv3_validation.cif.gz	50 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yv/5yv3 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/5yv3	HTTPS FTP

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Related structure data

Related structure data	5yurC 5yusC 5yutC 5yuuC 5yuvC 5yuwC 5yuxC 5yuyC 5yuzC 5yv0C 5yv1C 5yv2C 5yydC 5yyeC 5zlvC 6ig1C 4ir1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ig1-1 5yuu-1 5yv0-1 4irk-2 4ird-1 4q43-2 5yye-1 4irk-1 5yuz-1 4ir1-1 4irc-1 5yyd-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
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (10) #91 - Jul 2007 Thymine Dimers similarity (9) #168 - Dec 2013 DNA Helicase similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #253 - Jan 2021 Expressome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #227 - Nov 2018 Telomerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #135 - Mar 2011 Integrase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (2) #155 - Nov 2012 Vitamin D Receptor similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #23 - Nov 2001 DNA similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #131 - Nov 2010 Inteins similarity (1) #125 - May 2010 Parvoviruses similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

F: DNA polymerase IV

A: DNA polymerase IV

G: DTN1

H: DTN2

B: DTN1

C: DTN2

hetero molecules

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

1

F: DNA polymerase IV

G: DTN1

H: DTN2

hetero molecules

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

2

A: DNA polymerase IV

B: DTN1

C: DTN2

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.249, 57.038, 109.950
Angle α, β, γ (deg.)	90.00, 94.55, 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: K12 / Gene: dinB, dinP, b0231, JW0221 / Production host: Escherichia coli (E. coli) / References: UniProt: Q47155, DNA-directed DNA polymerase

#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: K12 / Gene: dinB, dinP, b0231, JW0221 / 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	DTN1 Mass: 5492.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria)
#3: DNA chain	DTN2 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, 422 molecules

#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-DPO / DIPHOSPHATE Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O₇P₂
#6: Chemical	ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₂O₁₄P₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.71 Å³/Da / Density % sol: 54.54 % 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 130 mm / Detector: CCD / Date: Sep 18, 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: 2.03→109.6 Å / Num. obs: 69290 / % possible obs: 98.3 % / Redundancy: 4.8 % / CC_1/2: 0.997 / R_merge(I) obs: 0.075 / Net I/σ(I): 12.3
Reflection shell	Resolution: 2.12→2.24 Å / R_merge(I) obs: 0.61 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8251 / CC_1/2: 0.807 / % possible all: 93.9

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4IR1

4ir1

Resolution: 2.03→54.802 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 30.61

	R_factor	Num. reflection	% reflection
R_free	0.2485	6675	5.09 %
R_work	0.2026	-	-
obs	0.2049	68895	97.17 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.03→54.802 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5374	1342	71	415	7202

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7077
X-RAY DIFFRACTION	f_angle_d	1.761	9858
X-RAY DIFFRACTION	f_dihedral_angle_d	22.242	4133
X-RAY DIFFRACTION	f_chiral_restr	0.059	1092
X-RAY DIFFRACTION	f_plane_restr	0.006	1032

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 (%)
2.03-2.0533	0.3707	214	0.3325	3982	X-RAY DIFFRACTION	94
2.0533-2.0775	0.3682	187	0.315	4136	X-RAY DIFFRACTION	97
2.0775-2.1028	0.3462	268	0.3104	4192	X-RAY DIFFRACTION	97
2.1028-2.1294	0.3414	208	0.3087	4075	X-RAY DIFFRACTION	97
2.1294-2.1575	0.3517	226	0.289	4036	X-RAY DIFFRACTION	96
2.1575-2.187	0.3561	216	0.2884	4050	X-RAY DIFFRACTION	95
2.187-2.2183	0.3379	241	0.2904	4008	X-RAY DIFFRACTION	95
2.2183-2.2514	0.3432	228	0.2872	4196	X-RAY DIFFRACTION	97
2.2514-2.2865	0.2849	187	0.2699	4256	X-RAY DIFFRACTION	99
2.2865-2.324	0.3508	225	0.265	4136	X-RAY DIFFRACTION	98
2.324-2.3641	0.2907	253	0.2555	4200	X-RAY DIFFRACTION	98
2.3641-2.4071	0.3382	236	0.2551	4181	X-RAY DIFFRACTION	99
2.4071-2.4534	0.2733	239	0.2486	4153	X-RAY DIFFRACTION	98
2.4534-2.5035	0.3288	203	0.2514	4171	X-RAY DIFFRACTION	97
2.5035-2.5579	0.28	220	0.2519	4188	X-RAY DIFFRACTION	97
2.5579-2.6174	0.3702	228	0.2514	4019	X-RAY DIFFRACTION	96
2.6174-2.6829	0.3328	212	0.267	4057	X-RAY DIFFRACTION	94
2.6829-2.7554	0.3366	233	0.2582	4108	X-RAY DIFFRACTION	97
2.7554-2.8365	0.2925	264	0.2495	4176	X-RAY DIFFRACTION	99
2.8365-2.928	0.2764	196	0.2444	4235	X-RAY DIFFRACTION	98
2.928-3.0327	0.2874	199	0.2432	4273	X-RAY DIFFRACTION	99
3.0327-3.1541	0.2761	219	0.2243	4198	X-RAY DIFFRACTION	98
3.1541-3.2976	0.2648	205	0.2124	4153	X-RAY DIFFRACTION	97
3.2976-3.4714	0.2058	190	0.1908	4113	X-RAY DIFFRACTION	96
3.4714-3.6889	0.2166	224	0.1791	4143	X-RAY DIFFRACTION	97
3.6889-3.9736	0.2272	263	0.1693	4212	X-RAY DIFFRACTION	99
3.9736-4.3734	0.219	179	0.1547	4294	X-RAY DIFFRACTION	99
4.3734-5.0058	0.219	235	0.1565	4125	X-RAY DIFFRACTION	97
5.0058-6.3054	0.2187	223	0.1723	4188	X-RAY DIFFRACTION	98
6.3054-54.8218	0.169	254	0.1548	4155	X-RAY DIFFRACTION	98

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	0.5706	-0.3161	0.1102	1.632	-0.2408	1.2959	-0.0308	0.1372	-0.0425	-0.2623	-0.0194	-0.5783	0.1037	-0.0552	-0.0013	0.229	-0.0214	0.0916	0.2305	-0.0251	0.4076	4.6767	-13.7707	-69.9716
2	0.3546	-0.361	0.3458	0.8763	-0.3237	0.3379	-0.1138	0.0696	0.4164	-0.1764	-0.0988	0.0835	-0.1938	-0.1544	-0.0002	0.2971	0.0093	-0.069	0.2802	0.0134	0.4291	-12.6995	3.4773	-69.1951
3	0.6258	-0.4592	0.0512	0.3387	-0.0731	0.7407	-0.1832	-0.1028	0.038	0.3498	0.0141	-0.2615	-0.1454	-0.0746	-0.0002	0.324	0.036	-0.0721	0.258	-0.0603	0.4475	1.2868	-14.5152	-44.315
4	1.3013	-0.0732	0.1374	1.9269	-0.7029	0.9174	-0.1309	-0.1996	0.2141	-0.301	0.2597	0.2266	0.2738	-0.4832	0.2441	0.1525	-0.0754	0.0204	0.5133	-0.1196	0.3155	-30.7676	-18.8732	-63.9164
5	0.7381	0.2553	0.1878	0.9631	0.04	0.6243	0.0398	-0.0296	-0.0409	0.3196	0.0196	-0.2398	0.1233	0.2121	-0.0003	0.5812	0.0519	-0.1125	0.4062	-0.002	0.3574	-27.9196	-8.0869	3.3428
6	0.3592	0.1149	-0.3226	0.8075	-0.2481	0.3161	0.2127	-0.0241	0.0824	0.009	-0.0952	-0.1948	-0.2453	0.2243	-0.0001	0.6345	-0.0217	-0.0034	0.4226	-0.055	0.3761	-25.5502	8.8239	-14.5638
7	0.6584	0.1159	0.1862	0.5546	-0.1334	0.1871	0.0988	0.0038	0.1186	-0.0974	0.0118	0.1428	-0.052	-0.0859	0.0001	0.5933	0.004	0.005	0.4008	0.0139	0.3357	-52.695	-8.854	-4.5626
8	0.9228	0.6046	-0.1831	0.9779	0.6576	1.5099	-0.0499	0.1859	-0.1165	0.0432	-0.0957	0.0026	0.1972	0.1361	0	0.4225	0.1366	0.0353	0.419	0.0078	0.2867	-27.6825	-14.7843	-32.4419
9	2.4896	0.4873	-0.0338	0.7006	0.2704	0.3395	-0.0192	-0.3325	-0.3247	0.012	-0.0961	-0.0887	-0.0027	-0.1375	-0.0543	0.1513	-0.0184	0.0632	0.2873	0.0271	0.2858	-17.7831	-22.869	-53.5842
10	0.8121	0.2022	0.1562	0.282	0.0306	0.0118	0.1342	-0.0214	-0.008	0.0901	-0.1359	-0.1225	0.0335	-0.2178	0.0002	0.5977	-0.0312	-0.0116	0.4442	-0.0617	0.316	-42.6531	-20.5213	-23.9822

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 860:874 OR RESID 900:900 ) ) OR ( CHAIN G AND RESID 838:854 ) OR ( CHAIN F AND RESID 901:903 )	H	860 - 874
12	X-RAY DIFFRACTION	9	( CHAIN H AND ( RESID 860:874 OR RESID 900:900 ) ) OR ( CHAIN G AND RESID 838:854 ) OR ( CHAIN F AND RESID 901:903 )	H	900
13	X-RAY DIFFRACTION	9	( CHAIN H AND ( RESID 860:874 OR RESID 900:900 ) ) OR ( CHAIN G AND RESID 838:854 ) OR ( CHAIN F AND RESID 901:903 )	G	838 - 854
14	X-RAY DIFFRACTION	9	( CHAIN H AND ( RESID 860:874 OR RESID 900:900 ) ) OR ( CHAIN G AND RESID 838:854 ) OR ( CHAIN F AND RESID 901:903 )	F	901 - 903
15	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 901:902 ) OR ( CHAIN C AND ( RESID 857:873 OR RESID 900:900 ) ) OR ( CHAIN B AND RESID 838:854 )	A	901 - 902
16	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 901:902 ) OR ( CHAIN C AND ( RESID 857:873 OR RESID 900:900 ) ) OR ( CHAIN B AND RESID 838:854 )	C	857 - 873
17	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 901:902 ) OR ( CHAIN C AND ( RESID 857:873 OR RESID 900:900 ) ) OR ( CHAIN B AND RESID 838:854 )	C	900
18	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 901:902 ) OR ( CHAIN C AND ( RESID 857:873 OR RESID 900:900 ) ) OR ( CHAIN B AND RESID 838:854 )	B	838 - 854

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