PDB-5yut: DNA polymerase IV - DNA ternary complex 3

ID or keywords:

Entry

Database: PDB / ID: 5yut

Title

DNA polymerase IV - DNA ternary complex 3

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 /

cytoplasm
Similarity search - Function

Biological species

Escherichia coli K-12 (bacteria)

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 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	Sep 5, 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.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	5yut.cif.gz	366.1 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yu/5yut ftp://data.pdbj.org/pub/pdb/validation_reports/yu/5yut	HTTPS FTP

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Related structure data

Related structure data	5yurC 5yusC 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	5yuy-1 1tue-2 3khh-1 1b4w-d 5yyd-2 1s0m-1 1c1j-d 1gri-d 1ecz-d 5zlv-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
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PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
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RecA and Rad51
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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)	86.750, 56.930, 110.210
Angle α, β, γ (deg.)	90.00, 95.12, 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: K12 / Gene: dinB, dinP, b0231, JW0221 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / 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 / Thymidine triphosphate Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₂O₁₄P₃
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 547 / 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: 54.1 % 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: 2.15→71.04 Å / Num. obs: 58767 / % possible obs: 100 % / Redundancy: 4.3 % / CC_1/2: 0.996 / R_merge(I) obs: 0.079 / Net I/σ(I): 10.8
Reflection shell	Resolution: 2.15→2.27 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.558 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8531 / CC_1/2: 0.734 / % possible all: 100

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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: 2.15→54.885 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 26.19
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.

	R_factor	Num. reflection	% reflection
R_free	0.2379	5766	5.05 %
R_work	0.1877	-	-
obs	0.1903	58726	99.91 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.15→54.885 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5374	1400	62	547	7383

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7102
X-RAY DIFFRACTION	f_angle_d	1.051	9900
X-RAY DIFFRACTION	f_dihedral_angle_d	19.281	4061
X-RAY DIFFRACTION	f_chiral_restr	0.056	1111
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 (%)
2.15-2.1744	0.3495	172	0.2975	3696	X-RAY DIFFRACTION	100
2.1744-2.2	0.3059	167	0.2706	3647	X-RAY DIFFRACTION	100
2.2-2.2269	0.3703	187	0.2789	3558	X-RAY DIFFRACTION	100
2.2269-2.255	0.3619	199	0.2857	3679	X-RAY DIFFRACTION	100
2.255-2.2847	0.3391	197	0.2672	3587	X-RAY DIFFRACTION	100
2.2847-2.316	0.3068	222	0.258	3515	X-RAY DIFFRACTION	100
2.316-2.3491	0.3438	200	0.2597	3658	X-RAY DIFFRACTION	100
2.3491-2.3842	0.347	191	0.2596	3610	X-RAY DIFFRACTION	100
2.3842-2.4214	0.2904	174	0.245	3604	X-RAY DIFFRACTION	100
2.4214-2.4611	0.2799	200	0.2391	3618	X-RAY DIFFRACTION	100
2.4611-2.5036	0.2485	164	0.2264	3625	X-RAY DIFFRACTION	100
2.5036-2.5491	0.2999	221	0.2263	3563	X-RAY DIFFRACTION	100
2.5491-2.5981	0.283	204	0.2247	3655	X-RAY DIFFRACTION	100
2.5981-2.6512	0.2614	193	0.2205	3591	X-RAY DIFFRACTION	100
2.6512-2.7088	0.3009	225	0.2155	3657	X-RAY DIFFRACTION	100
2.7088-2.7718	0.2556	185	0.2157	3513	X-RAY DIFFRACTION	100
2.7718-2.8411	0.2544	225	0.2124	3644	X-RAY DIFFRACTION	100
2.8411-2.9179	0.2493	175	0.2082	3610	X-RAY DIFFRACTION	100
2.9179-3.0038	0.2822	173	0.2027	3645	X-RAY DIFFRACTION	100
3.0038-3.1007	0.2891	188	0.1941	3613	X-RAY DIFFRACTION	100
3.1007-3.2115	0.2614	185	0.1923	3621	X-RAY DIFFRACTION	100
3.2115-3.3401	0.232	173	0.1773	3701	X-RAY DIFFRACTION	100
3.3401-3.4921	0.1832	169	0.1661	3569	X-RAY DIFFRACTION	100
3.4921-3.6762	0.2402	195	0.1684	3625	X-RAY DIFFRACTION	100
3.6762-3.9064	0.2184	200	0.1636	3578	X-RAY DIFFRACTION	100
3.9064-4.208	0.2293	181	0.1455	3632	X-RAY DIFFRACTION	100
4.208-4.6312	0.2017	189	0.1418	3635	X-RAY DIFFRACTION	100
4.6312-5.3009	0.1815	199	0.1429	3612	X-RAY DIFFRACTION	100
5.3009-6.6767	0.2014	208	0.1774	3590	X-RAY DIFFRACTION	100
6.6767-54.903	0.145	205	0.1487	3568	X-RAY DIFFRACTION	99

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	0.375	-0.1306	0.1551	0.8967	0.2904	0.7962	-0.036	0.1554	-0.088	-0.196	0.0088	-0.3824	0.0117	-0.0012	0.0002	0.1639	-0.0113	0.0574	0.1934	-0.0243	0.333	5.2633	-14.8598	-70.1198
2	0.2089	-0.2308	0.1805	0.4633	-0.257	0.2129	-0.0497	0.1256	0.324	-0.1336	-0.1697	-0.0223	-0.0759	-0.0786	-0	0.2287	0.0212	-0.0734	0.1963	-0.0037	0.395	-12.1494	2.3359	-69.2885
3	0.3639	-0.1838	0.0613	0.2985	0.0521	0.0937	-0.2355	-0.0443	0.0379	0.3637	0.0606	-0.1884	-0.0551	-0.0398	-0.0039	0.2339	0.0378	-0.0746	0.2066	-0.0323	0.3831	1.7807	-15.4853	-44.3525
4	0.9979	0.3034	0.102	0.6472	-0.3185	0.4532	-0.1269	-0.2321	0.1292	-0.126	0.0436	0.1195	0.1233	-0.336	0.0085	-0.0477	-0.0968	0.0607	0.4423	-0.1973	0.2999	-30.3335	-19.7155	-64.048
5	0.5037	0.2379	0.0469	0.6907	-0.1913	0.3948	0.0472	-0.0712	-0.0476	0.2523	0.0132	-0.116	0.1163	0.1513	-0.0001	0.402	0.0762	-0.0544	0.3061	-0.015	0.22	-28.2024	-9.1976	3.4332
6	0.1988	0.034	-0.2169	0.3954	0.1215	0.2931	0.1055	0.0185	0.0534	0.0282	-0.0429	-0.0735	-0.3169	0.2187	0	0.4914	-0.0522	0.0241	0.3045	-0.0159	0.2566	-25.7238	7.746	-14.3333
7	0.5084	-0.128	0.0296	0.4492	-0.0992	0.2575	0.0183	-0.0104	0.1109	-0.0347	0.0128	0.1112	0.0895	-0.1809	-0.0001	0.4422	-0.0108	0.0193	0.3126	0.0098	0.1851	-52.909	-9.9093	-4.6472
8	0.6609	0.2441	-0.0474	0.5019	0.4977	1.2453	-0.0484	0.0767	0.0334	0.1345	-0.0527	-0.0502	0.2074	0.2303	-0.0045	0.2548	0.0964	0.0409	0.2543	0.0156	0.1309	-27.5889	-15.7124	-32.4056
9	0.9815	0.2028	0.3528	0.6276	-0.2097	0.2417	-0.049	-0.1407	-0.1048	0.0047	-0.0816	-0.0333	0.0366	-0.145	-0.0289	0.1652	-0.0123	0.0809	0.2358	-0.0327	0.2614	-18.4011	-25.8687	-51.3475
10	0.3988	0.2145	0.2823	0.1582	0.214	0.2792	0.0914	-0.0769	-0.0474	-0.0166	-0.1054	-0.0272	0.0364	-0.1885	-0	0.4502	-0.0498	-0.0068	0.3245	-0.0219	0.2505	-42.5465	-20.864	-23.9407

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 858 through 873 ) or chain 'G' and (resid 837 through 854) or chain 'F' and (resid 900 through 902)
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 837 through 854 ) or chain 'C' and (resid 857 through 873) or chain 'A' and (resid 900 through 902)

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