PDB-5yur: DNA polymerase IV - DNA ternary complex 1

ID or keywords:

Entry

Database: PDB / ID: 5yur

Title

DNA polymerase IV - DNA ternary complex 1

Components

DNA polymerase IV
DTN

Keywords

DNA BINDING PROTEIN/DNA / DNA POLYMERASE / 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)

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.035 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	Aug 29, 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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5yur.cif.gz	359.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5yur.ent.gz	287 KB	Display	PDB format
PDBx/mmJSON format	5yur.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5yur_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5yur_full_validation.pdf.gz	1.2 MB	Display
Data in XML	5yur_validation.xml.gz	33.5 KB	Display
Data in CIF	5yur_validation.cif.gz	48.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yu/5yur ftp://data.pdbj.org/pub/pdb/validation_reports/yu/5yur	HTTPS FTP

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Related structure data

Related structure data	5yusC 5yutC 5yuuC 5yuvC 5yuwC 5yuxC 5yuyC 5yuzC 5yv0C 5yv1C 5yv2C 5yv3C 5yydC 5yyeC 5zlvC 6ig1C 4ir1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1huo-1 3uxp-2 1huo-2 5yv1-1 6ig1-1 4gc6-d 2r8i-d 2v4q-d 2asj-2 3v6j-2 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

Related items in Molecule of the Month

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TATA-Binding Protein
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Deposited unit

F: DNA polymerase IV

A: DNA polymerase IV

G: DTN

H: DTN

B: DTN

C: DTN

hetero molecules

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

1

F: DNA polymerase IV

G: DTN

H: DTN

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: DTN

C: DTN

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)	86.560, 57.010, 110.431
Angle α, β, γ (deg.)	90.00, 94.79, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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 / Gene: dinB, dinP, b0231, JW0221 / Plasmid: pGEX-6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: Q47155, DNA-directed DNA polymerase
#2: DNA chain	DTN Mass: 5492.554 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Chemical	ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₂O₁₄P₃
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.68 Å³/Da / Density % sol: 54.18 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/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
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
Detector	Type: MAR CCD 130 mm / Detector: CCD / Date: Sep 16, 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: 2.035→65.3 Å / Num. obs: 69238 / % possible obs: 99.3 % / Redundancy: 3.6 % / Net I/σ(I): 8.4
Reflection shell	Resolution: 2.04→2.15 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.604 / Mean I/σ(I) obs: 2 / Num. unique obs: 36551 / CC_1/2: 0.733 / R_pim(I) all: 0.362 / % possible all: 99.6

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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: 2.035→65.292 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 31.27 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.

	R_factor	Num. reflection	% reflection
R_free	0.2517	6528	5.03 %
R_work	0.2039	-	-
obs	0.2064	64860	96.19 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.035→65.292 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5373	1224	60	434	7091

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6904
X-RAY DIFFRACTION	f_angle_d	1.074	9594
X-RAY DIFFRACTION	f_dihedral_angle_d	20.592	3973
X-RAY DIFFRACTION	f_chiral_restr	0.057	1077
X-RAY DIFFRACTION	f_plane_restr	0.006	1024

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 (%)
2.035-2.0581	0.3676	219	0.3421	4063	X-RAY DIFFRACTION	97
2.0581-2.0824	0.3868	203	0.3329	4166	X-RAY DIFFRACTION	97
2.0824-2.1077	0.3209	235	0.3186	4145	X-RAY DIFFRACTION	97
2.1077-2.1344	0.3639	179	0.3109	4098	X-RAY DIFFRACTION	97
2.1344-2.1625	0.332	207	0.2941	4186	X-RAY DIFFRACTION	97
2.1625-2.1921	0.3618	214	0.2906	4066	X-RAY DIFFRACTION	96
2.1921-2.2235	0.3338	221	0.2898	3934	X-RAY DIFFRACTION	93
2.2235-2.2567	0.3529	213	0.2907	3918	X-RAY DIFFRACTION	90
2.2567-2.2919	0.323	183	0.2776	3931	X-RAY DIFFRACTION	93
2.2919-2.3295	0.3251	223	0.2655	4101	X-RAY DIFFRACTION	97
2.3295-2.3697	0.3108	261	0.2691	4240	X-RAY DIFFRACTION	98
2.3697-2.4128	0.3617	221	0.2766	4201	X-RAY DIFFRACTION	99
2.4128-2.4592	0.3176	246	0.2638	4159	X-RAY DIFFRACTION	98
2.4592-2.5094	0.2932	205	0.2534	4164	X-RAY DIFFRACTION	97
2.5094-2.5639	0.306	213	0.2509	4157	X-RAY DIFFRACTION	97
2.5639-2.6236	0.3851	235	0.2542	4102	X-RAY DIFFRACTION	96
2.6236-2.6892	0.3153	211	0.257	4048	X-RAY DIFFRACTION	95
2.6892-2.7619	0.2787	216	0.2468	3885	X-RAY DIFFRACTION	91
2.7619-2.8432	0.2842	251	0.2473	4010	X-RAY DIFFRACTION	95
2.8432-2.9349	0.2819	206	0.2346	4231	X-RAY DIFFRACTION	99
2.9349-3.0398	0.2948	195	0.2251	4263	X-RAY DIFFRACTION	98
3.0398-3.1615	0.2771	223	0.2224	4145	X-RAY DIFFRACTION	98
3.1615-3.3054	0.2625	206	0.2058	4201	X-RAY DIFFRACTION	98
3.3054-3.4797	0.1954	189	0.1895	4101	X-RAY DIFFRACTION	96
3.4797-3.6977	0.2552	213	0.1913	3932	X-RAY DIFFRACTION	93
3.6977-3.9831	0.25	268	0.179	4189	X-RAY DIFFRACTION	98
3.9831-4.3839	0.2074	171	0.1568	4257	X-RAY DIFFRACTION	98
4.3839-5.0181	0.1994	236	0.1582	4103	X-RAY DIFFRACTION	97
5.0181-6.3214	0.218	219	0.1765	4066	X-RAY DIFFRACTION	95
6.3214-65.3259	0.1893	246	0.1576	4130	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	0.0796	-0.1112	0.1387	0.298	0.0403	0.57	-0.0264	0.1105	-0.2092	-0.1385	0.0888	-0.8294	-0.0507	-0.0137	0.0059	0.273	-0.0549	0.0745	0.2728	-0.063	0.6829	4.9951	-14.2651	-70.2946
2	0.1396	-0.0432	0.1255	0.435	-0.129	0.0873	-0.241	-0.0574	0.4771	-0.1168	-0.1113	0.0409	-0.2868	-0.0873	-0.0007	0.3609	0.0226	-0.1182	0.2813	-0.0316	0.5775	-12.5029	2.9482	-69.4428
3	0.2056	-0.1907	0.0919	0.1493	-0.0708	0.3012	-0.2122	-0.0248	-0.1622	0.3831	-0.159	-0.4493	-0.2723	-0.0734	-0.0038	0.4054	0.0344	-0.1788	0.3101	-0.0377	0.6913	1.4478	-15.0414	-44.5458
4	1.1712	0.2171	-0.1757	1.8028	-1.1411	1.2333	-0.273	-0.4141	0.5696	-0.7987	0.4982	0.2987	0.5636	-0.8605	0.3837	0.0898	-0.0586	0.1356	0.6649	-0.294	0.2583	-30.6846	-19.3206	-64.1165
5	0.2111	0.0606	0.0322	0.2627	-0.0224	0.2874	0.1258	-0.1228	-0.2958	0.3342	0.0252	-0.3109	0.383	0.4865	-0.0002	0.7579	0.1269	-0.1332	0.6004	-0.0481	0.4641	-28.0145	-8.577	3.3443
6	0.1152	0.1178	-0.1249	0.1992	0.0019	0.1837	0.2964	-0.0181	-0.0119	-0.1368	-0.0072	-0.4278	-0.4802	0.4902	0.0001	0.7561	-0.0396	0.0236	0.5391	-0.0858	0.4897	-25.6948	8.3391	-14.6286
7	0.1227	0.0303	0.0017	0.186	-0.0712	0.1158	0.0656	-0.1063	0.1332	-0.0675	0.0102	0.4465	0.1314	-0.4035	-0.0007	0.7511	-0.0342	0.0327	0.5459	0.0402	0.3582	-52.7207	-9.4956	-4.4903
8	0.4727	0.0908	0.0458	0.38	0.3525	0.7175	-0.0563	0.2236	-0.0499	0.1032	-0.0603	-0.146	0.2431	0.2617	-0.0003	0.5512	0.2206	0.0317	0.4671	-0.0303	0.2952	-27.6924	-15.2766	-32.5025
9	1.161	-0.0126	0.2906	0.1547	0.1633	0.1723	-0.134	-0.2185	-0.2126	-0.1252	0.0287	-0.1274	0.05	-0.2423	-0.0059	0.2377	-0.0116	0.0962	0.3975	-0.0429	0.372	-18.4334	-23.4846	-53.9038
10	0.2335	-0.0635	-0.1341	0.1871	0.1183	0.0243	0.1327	-0.1379	-0.2291	0.0647	-0.1763	-0.1799	0.105	-0.2721	-0.0025	0.6736	-0.0067	-0.0452	0.5015	-0.0557	0.4116	-42.9056	-21.8463	-23.9198

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 862 through 873 ) or chain 'G' and (resid 839 through 853) or chain 'F' and (resid 900 through 901)
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 839 through 854 ) or chain 'C' and (resid 857 through 873) or chain 'A' and (resid 900) or chain 'A' and (resid 902)

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