PDB-5yuy: DNA polymerase IV - DNA ternary complex 9

ID or keywords:

Entry

Database: PDB / ID: 5yuy

Title

DNA polymerase IV - DNA ternary complex 9

Components

DNA polymerase IV
DTN
DTN1

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: 1.74 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	Oct 17, 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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PDBx/mmCIF format	5yuy.cif.gz	387.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5yuy_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	5yuy_full_validation.pdf.gz	1.2 MB	Display
Data in XML	5yuy_validation.xml.gz	41.7 KB	Display
Data in CIF	5yuy_validation.cif.gz	63.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yu/5yuy ftp://data.pdbj.org/pub/pdb/validation_reports/yu/5yuy	HTTPS FTP

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Related structure data

Related structure data	5yurC 5yusC 5yutC 5yuuC 5yuvC 5yuwC 5yuxC 5yuzC 5yv0C 5yv1C 5yv2C 5yv3C 5yydC 5yyeC 5zlvC 6ig1C 4ir1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5yut-1 3khh-1 4ird-1 4irk-2 5yyd-2 1ecz-d 3b6a-4 1s0m-1 5yuz-1 4r8u-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

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wwPDB /

NCBI

Related items in Molecule of the Month

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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: DTN1

H: DTN

B: DTN1

C: DTN

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: DTN

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: DTN

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.460, 57.050, 110.170
Angle α, β, γ (deg.)	90.00, 95.03, 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	DTN1 Mass: 5492.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria)
#3: DNA chain	DTN 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, 1007 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.: 2 / 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.: 999 / 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: 2.66 Å³/Da / Density % sol: 53.76 % 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 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: 1.74→54.87 Å / Num. obs: 110068 / % possible obs: 99.9 % / Redundancy: 3.8 % / CC_1/2: 0.996 / R_merge(I) obs: 0.06 / Net I/σ(I): 12.1
Reflection shell	Resolution: 1.74→1.83 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.587 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 15993 / CC_1/2: 0.751 / % 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: 1.74→44.542 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 24.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2153	10768	5.02 %
R_work	0.1881	-	-
obs	0.1895	110068	99.77 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.74→44.542 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5382	1440	80	999	7901

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7223
X-RAY DIFFRACTION	f_angle_d	1.04	10080
X-RAY DIFFRACTION	f_dihedral_angle_d	22.125	4201
X-RAY DIFFRACTION	f_chiral_restr	0.054	1115
X-RAY DIFFRACTION	f_plane_restr	0.006	1038

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 (%)
1.74-1.7598	0.3759	350	0.3555	6729	X-RAY DIFFRACTION	99
1.7598-1.7805	0.3513	393	0.3016	6863	X-RAY DIFFRACTION	100
1.7805-1.8022	0.3406	396	0.3038	6693	X-RAY DIFFRACTION	100
1.8022-1.825	0.3087	345	0.2801	6801	X-RAY DIFFRACTION	100
1.825-1.849	0.3334	339	0.2781	6901	X-RAY DIFFRACTION	100
1.849-1.8744	0.3318	337	0.2725	6764	X-RAY DIFFRACTION	100
1.8744-1.9011	0.3106	355	0.2663	6816	X-RAY DIFFRACTION	100
1.9011-1.9295	0.3036	358	0.2549	6794	X-RAY DIFFRACTION	100
1.9295-1.9597	0.2596	376	0.2381	6876	X-RAY DIFFRACTION	100
1.9597-1.9918	0.2705	386	0.2372	6729	X-RAY DIFFRACTION	100
1.9918-2.0261	0.2796	354	0.2308	6839	X-RAY DIFFRACTION	100
2.0261-2.063	0.2325	342	0.2258	6819	X-RAY DIFFRACTION	100
2.063-2.1027	0.2623	332	0.2167	6886	X-RAY DIFFRACTION	100
2.1027-2.1456	0.2548	324	0.2161	6817	X-RAY DIFFRACTION	100
2.1456-2.1922	0.2405	328	0.1945	6834	X-RAY DIFFRACTION	100
2.1922-2.2432	0.2331	341	0.1983	6810	X-RAY DIFFRACTION	100
2.2432-2.2993	0.2601	422	0.1998	6812	X-RAY DIFFRACTION	100
2.2993-2.3615	0.2419	355	0.194	6739	X-RAY DIFFRACTION	100
2.3615-2.431	0.2271	345	0.1949	6853	X-RAY DIFFRACTION	100
2.431-2.5094	0.2189	337	0.1981	6814	X-RAY DIFFRACTION	100
2.5094-2.5991	0.2506	414	0.2	6846	X-RAY DIFFRACTION	100
2.5991-2.7032	0.2335	378	0.2028	6758	X-RAY DIFFRACTION	100
2.7032-2.8262	0.2262	402	0.1908	6718	X-RAY DIFFRACTION	100
2.8262-2.9751	0.197	329	0.1851	6910	X-RAY DIFFRACTION	100
2.9751-3.1615	0.224	355	0.1711	6810	X-RAY DIFFRACTION	100
3.1615-3.4055	0.1798	304	0.1584	6829	X-RAY DIFFRACTION	100
3.4055-3.7481	0.167	365	0.1575	6832	X-RAY DIFFRACTION	100
3.7481-4.29	0.1888	354	0.1482	6822	X-RAY DIFFRACTION	100
4.29-5.4035	0.1767	386	0.1557	6776	X-RAY DIFFRACTION	100
5.4035-44.557	0.1616	366	0.1776	6457	X-RAY DIFFRACTION	95

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	1.4348	-0.0772	0.516	1.6612	0.1116	2.0863	-0.0605	-0.1692	-0.0613	0.1995	0.0085	0.5438	0.0416	-0.1618	0.0477	0.1436	0.0131	0.0571	0.1784	0.0146	0.3767	71.7296	12.6261	179.7331
2	0.7644	0.1182	0.5015	1.4853	-0.141	0.5748	-0.0742	-0.1303	0.5843	0.2636	-0.213	-0.0234	-0.2907	0.1698	0.1899	0.2411	-0.0302	-0.1242	0.2149	0.011	0.4718	89.0339	29.8109	179.0614
3	1.5771	0.5427	0.3054	1.3187	0.0533	0.8696	-0.2354	0.165	0.1087	-0.5061	0.0567	0.2357	-0.1027	0.0612	0.1382	0.2484	-0.0439	-0.1104	0.1979	0.0493	0.417	75.0196	11.9953	154.0894
4	1.6448	-0.59	0.0999	1.0916	0.6719	1.2772	-0.1434	0.3341	0.1522	0.2483	0.05	-0.2486	0.359	0.6303	0.0892	0.0053	0.0734	0.0808	0.4617	0.2075	0.2583	107.0991	7.8169	173.8678
5	1.5	-0.2159	0.3026	1.3862	-0.049	1.3047	-0.0053	0.1172	-0.0167	-0.2882	0.0192	0.2158	0.134	-0.1553	-0.0095	0.398	-0.0469	-0.0565	0.2727	-0.0002	0.1995	104.9643	18.2908	106.3067
6	0.892	-0.2966	-0.3313	1.3716	-0.024	1.328	0.0933	-0.0897	0.2042	0.0018	-0.0599	0.1432	-0.5104	-0.3836	-0.0411	0.4464	0.064	0.0138	0.2543	0.0021	0.2287	102.4661	35.2576	124.05
7	1.1384	0.0718	-0.0349	1.6232	0.4656	1.1138	0.0208	0.0091	0.068	0.1046	0.0003	-0.3421	0.1214	0.1755	-0.041	0.4023	0.0043	0.0063	0.28	0.0057	0.2038	129.6481	17.7078	114.4019
8	1.2838	-0.0241	0.052	1.7446	-0.2758	2.406	-0.0617	-0.0395	-0.1086	-0.1887	-0.0297	0.1255	0.2876	-0.3807	0.1	0.3184	-0.1006	0.0339	0.3415	-0.0155	0.1883	104.3588	11.7257	142.068
9	1.2497	-0.4512	0.2496	1.5888	1.0932	0.9861	-0.0764	0.3057	-0.1673	-0.0809	-0.0906	-0.0168	0.131	0.2509	0.1312	0.2123	0.0331	0.0949	0.3114	0.0431	0.2907	94.49	2.6988	161.9173
10	1.0269	-0.9846	0.7964	1.0833	-0.7123	0.472	0.0949	0.0923	-0.0706	0.0132	-0.1167	0.0104	0.0016	0.1932	0.0088	0.3971	0.0242	0.0275	0.2981	0.0107	0.1665	118.5295	7.7544	132.7929

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 874 ) or chain 'G' and (resid 837 through 854) or chain 'F' and (resid 901 through 903)
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 837 through 854 ) or chain 'C' and (resid 857 through 874) or chain 'A' and (resid 901 through 903)

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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, 1007 molecules

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules FA

-
DNA chain , 2 types, 4 molecules GBHC

-
Non-polymers , 4 types, 1007 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

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Yorodumi