PDB-5yyd: DNA polymerase IV - ternary complex 15

ID or keywords:

Entry

Database: PDB / ID: 5yyd

Title

DNA polymerase IV - ternary complex 15

Components

DNA polymerase IV
DTN2

Keywords

DNA BINDING PROTEIN/DNA /

DNA POLYMERASE /

DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

SOS response / DNA synthesis involved in DNA repair / error-free translesion synthesis / 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 (E. coli)

Escherichia coli K-12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 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	Dec 8, 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 / 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_label_asym_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5yyd.cif.gz	362.8 KB	Display	PDBx/mmCIF format
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Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yy/5yyd ftp://data.pdbj.org/pub/pdb/validation_reports/yy/5yyd	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 5yyeC 5zlvC 6ig1C 4ir1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4irc-1 5yye-1 5yuw-2 6ig1-1 5yv2-1 4irk-1 4irk-2 5yv1-1 5yus-1 5yv0-1 4q44-2 3gil-2 4ir9-1 5yv3-1 3khh-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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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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

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Deposited unit

F: DNA polymerase IV

A: DNA polymerase IV

G: DTN2

H: DTN2

B: DTN2

C: DTN2

hetero molecules

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

1

F: DNA polymerase IV

G: DTN2

H: DTN2

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: DTN2

C: DTN2

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)	86.650, 57.050, 110.330
Angle α, β, γ (deg.)	90.00, 94.94, 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 (E. coli) / Strain: K12 / Gene: dinB, dinP, b0231, JW0221 / Production host: Escherichia coli (E. coli) / References: UniProt: Q47155, DNA-directed DNA polymerase
#2: DNA chain	DTN2 Mass: 5492.554 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria)
#3: Chemical	ChemComp-TTW / 5'-O-[hydroxy{[hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]thymidine Mass: 481.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₈N₃O₁₃P₃
#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 / Water Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.83 Å³/Da / Density % sol: 56.51 % 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: ID29 / Wavelength: 0.97264 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97264 Å / Relative weight: 1
Reflection	Resolution: 2.05→86.33 Å / Num. obs: 67838 / % possible obs: 99.4 % / Redundancy: 3.6 % / CC_1/2: 0.999 / Net I/σ(I): 12
Reflection shell	Resolution: 2.05→2.16 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9744 / CC_1/2: 0.725 / % possible all: 99.3

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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: 2.05→70.924 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 27.84
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2372	6488	5.13 %	RANDOM
R_work	0.1953	-	-	-
obs	0.1975	67314	95.75 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.05→70.924 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5374	1287	60	395	7116

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6975
X-RAY DIFFRACTION	f_angle_d	1.074	9702
X-RAY DIFFRACTION	f_dihedral_angle_d	20.764	4046
X-RAY DIFFRACTION	f_chiral_restr	0.058	1084
X-RAY DIFFRACTION	f_plane_restr	0.006	1027

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 (%)
2.05-2.0733	0.3907	232	0.3225	4009	X-RAY DIFFRACTION	96
2.0733-2.0977	0.388	193	0.328	3958	X-RAY DIFFRACTION	95
2.0977-2.1233	0.3495	221	0.3192	3968	X-RAY DIFFRACTION	95
2.1233-2.1502	0.3299	229	0.2933	3871	X-RAY DIFFRACTION	94
2.1502-2.1784	0.3358	238	0.281	3944	X-RAY DIFFRACTION	93
2.1784-2.2083	0.2771	226	0.2717	3831	X-RAY DIFFRACTION	92
2.2083-2.2398	0.3289	207	0.2728	3915	X-RAY DIFFRACTION	95
2.2398-2.2733	0.314	199	0.2722	4042	X-RAY DIFFRACTION	96
2.2733-2.3088	0.3079	207	0.2638	3975	X-RAY DIFFRACTION	96
2.3088-2.3467	0.3094	204	0.2673	4113	X-RAY DIFFRACTION	96
2.3467-2.3871	0.313	229	0.2561	3987	X-RAY DIFFRACTION	96
2.3871-2.4305	0.296	241	0.2474	3962	X-RAY DIFFRACTION	97
2.4305-2.4773	0.2504	215	0.2423	4093	X-RAY DIFFRACTION	96
2.4773-2.5279	0.2831	209	0.2436	3952	X-RAY DIFFRACTION	96
2.5279-2.5828	0.3229	221	0.2436	3934	X-RAY DIFFRACTION	95
2.5828-2.6429	0.3364	197	0.2551	3910	X-RAY DIFFRACTION	94
2.6429-2.709	0.287	224	0.2354	3898	X-RAY DIFFRACTION	93
2.709-2.7822	0.2531	238	0.2194	3986	X-RAY DIFFRACTION	97
2.7822-2.8641	0.2457	216	0.231	4076	X-RAY DIFFRACTION	97
2.8641-2.9566	0.2971	200	0.218	4088	X-RAY DIFFRACTION	98
2.9566-3.0622	0.2645	200	0.2148	4064	X-RAY DIFFRACTION	97
3.0622-3.1848	0.2541	231	0.2096	4108	X-RAY DIFFRACTION	97
3.1848-3.3298	0.2377	184	0.1927	4092	X-RAY DIFFRACTION	97
3.3298-3.5053	0.1854	195	0.1814	3871	X-RAY DIFFRACTION	93
3.5053-3.7249	0.2308	220	0.1819	4094	X-RAY DIFFRACTION	98
3.7249-4.0125	0.2397	257	0.172	4093	X-RAY DIFFRACTION	99
4.0125-4.4163	0.2171	164	0.1501	4154	X-RAY DIFFRACTION	98
4.4163-5.0552	0.2013	228	0.1486	3962	X-RAY DIFFRACTION	95
5.0552-6.3683	0.1944	218	0.1629	4065	X-RAY DIFFRACTION	97
6.3683-70.9667	0.1604	245	0.1491	3996	X-RAY DIFFRACTION	96

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	1.6664	0.0652	1.0862	2.859	-0.5084	4.0514	-0.0867	0.3591	-0.1521	-0.3205	-0.0414	-0.756	0.2134	0.2015	0.1344	0.2478	-0.0178	0.0728	0.2983	-0.0473	0.5616	5.1187	-14.8662	-70.2172
2	1.6941	-0.6395	0.3047	3.5772	0.4403	1.6121	-0.1408	0.1625	0.6194	-0.3766	-0.2054	0.2372	-0.4248	-0.2658	0.3049	0.3886	0.0474	-0.1742	0.3631	-0.0376	0.5924	-12.3629	2.3854	-69.2799
3	3.0001	-1.6768	-0.4455	2.1419	-0.0876	2.2331	-0.2874	-0.3093	0.0273	0.6138	0.0643	-0.3065	-0.1602	-0.041	0.23	0.367	0.0385	-0.1791	0.3176	-0.0444	0.6181	1.6151	-15.5876	-44.4198
4	3.8591	0.2971	0.9556	3.0368	-0.2913	2.019	-0.3289	-0.689	0.5244	-0.3793	0.2665	0.3074	0.4135	-0.8776	0.0609	0.1919	-0.1209	0.0448	0.8087	-0.2453	0.4571	-30.5014	-19.9733	-64.0611
5	2.2082	-0.0877	-0.1374	1.9905	0.0902	1.8419	0.0508	-0.2436	-0.2311	0.4562	0.0884	-0.3932	0.4064	0.5358	-0.0932	0.6674	0.1533	-0.1734	0.5772	-0.0381	0.4162	-28.0974	-9.2255	3.4613
6	2.4525	0.4377	-1.0571	4.2696	0.575	2.2788	0.2173	-0.0376	0.229	-0.0179	0.0874	-0.4775	-0.6472	0.5476	-0.2986	0.555	-0.0315	0.0443	0.4595	-0.0606	0.3492	-25.8009	7.6268	-14.469
7	2.4228	0.4821	0.2573	3.2104	-0.8998	2.6523	0.0336	0.0086	0.1205	-0.13	0.0584	0.2769	0.1431	-0.5378	-0.0539	0.6259	0.0186	0.0038	0.5535	0.0442	0.3415	-52.8332	-10.1328	-4.5624
8	2.3151	-0.4107	-0.0768	3.361	0.0474	4.5938	-0.1295	0.0745	-0.2397	0.1979	-0.0024	-0.2802	0.7001	0.6195	0.1332	0.5075	0.2247	0.0352	0.5609	0.01	0.3319	-27.651	-15.8981	-32.4429
9	3.442	1.1874	0.283	2.5332	-1.2552	1.6887	-0.1062	-0.5495	-0.5017	0.173	-0.0961	-0.0075	0.1391	-0.4224	0.2071	0.3147	-0.0073	0.1004	0.5013	-0.0687	0.4526	-18.4003	-24.6362	-53.0259
10	2.1314	2.4283	0.9944	2.8706	1.7243	0.284	0.1515	-0.0016	-0.2287	0.0797	-0.1849	-0.1273	0.3531	-0.3959	0.0189	0.6926	-0.0295	-0.0714	0.5188	-0.0481	0.381	-42.2855	-21.1503	-23.7156

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 873 ) or chain 'G' and (resid 838 through 854) or chain 'F' and (resid 900 through 901)
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 838 through 854 ) or chain 'C' and (resid 858 through 873) or chain 'A' and (resid 900 through 901)

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