PDB-5yye: DNA polymerase IV - ternary complex 16

ID or keywords:

Entry

Database: PDB / ID: 5yye

Title

DNA polymerase IV - ternary complex 16

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 / error-free translesion synthesis / DNA synthesis involved in DNA repair / 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: 2.325 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 / 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.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_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	5yye.cif.gz	359.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5yye.ent.gz	287.8 KB	Display	PDB format
PDBx/mmJSON format	5yye.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5yye_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5yye_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5yye_validation.xml.gz	30.3 KB	Display
Data in CIF	5yye_validation.cif.gz	41.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yy/5yye ftp://data.pdbj.org/pub/pdb/validation_reports/yy/5yye	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 5yydC 5zlvC 6ig1C 4ir1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5yv1-1 4q44-2 5yyd-1 4irc-1 6ig1-1 3t5k-d 4ir9-1 5yv2-1 4irk-2 5yuw-2 5yuz-1 5yv3-1 6vnp-1 2c2d-d 3gil-2 4irk-1 4ird-1 4ir1-1 4gc6-d 2c2r-d 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 /

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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)	86.300, 56.950, 110.710
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 (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-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.8 Å³/Da / Density % sol: 56 % 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: 2.325→86 Å / Num. obs: 46597 / % possible obs: 99.6 % / Redundancy: 3.6 % / CC_1/2: 0.998 / Net I/σ(I): 9
Reflection shell	Resolution: 2.33→2.45 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 6752 / CC_1/2: 0.674 / % possible all: 99.8

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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: 2.325→65.236 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0.13 / Phase error: 30.94
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2551	4472	5.13 %	RANDOM
R_work	0.2002	-	-	-
obs	0.2031	43574	96.38 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.325→65.236 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5374	1338	62	97	6871

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7031
X-RAY DIFFRACTION	f_angle_d	1.105	9791
X-RAY DIFFRACTION	f_dihedral_angle_d	22.132	4072
X-RAY DIFFRACTION	f_chiral_restr	0.056	1092
X-RAY DIFFRACTION	f_plane_restr	0.006	1030

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 (%)
2.325-2.3514	0.3353	184	0.339	2860	X-RAY DIFFRACTION	98
2.3514-2.3791	0.4419	136	0.3253	2745	X-RAY DIFFRACTION	97
2.3791-2.4081	0.4087	176	0.3216	2715	X-RAY DIFFRACTION	96
2.4081-2.4386	0.329	138	0.3168	2784	X-RAY DIFFRACTION	97
2.4386-2.4707	0.2887	170	0.3028	2793	X-RAY DIFFRACTION	96
2.4707-2.5045	0.3416	144	0.2981	2676	X-RAY DIFFRACTION	95
2.5045-2.5403	0.3869	132	0.3063	2723	X-RAY DIFFRACTION	96
2.5403-2.5782	0.3412	145	0.3042	2626	X-RAY DIFFRACTION	92
2.5782-2.6185	0.3969	154	0.308	2667	X-RAY DIFFRACTION	93
2.6185-2.6615	0.3893	127	0.3063	2744	X-RAY DIFFRACTION	96
2.6615-2.7073	0.381	170	0.2884	2857	X-RAY DIFFRACTION	97
2.7073-2.7566	0.3478	154	0.2709	2747	X-RAY DIFFRACTION	98
2.7566-2.8096	0.2947	180	0.2589	2727	X-RAY DIFFRACTION	97
2.8096-2.8669	0.3316	138	0.2487	2816	X-RAY DIFFRACTION	98
2.8669-2.9293	0.3298	146	0.2596	2707	X-RAY DIFFRACTION	96
2.9293-2.9974	0.3354	132	0.2415	2818	X-RAY DIFFRACTION	96
2.9974-3.0724	0.3262	132	0.2421	2657	X-RAY DIFFRACTION	94
3.0724-3.1555	0.2982	141	0.236	2750	X-RAY DIFFRACTION	95
3.1555-3.2483	0.2839	139	0.2293	2752	X-RAY DIFFRACTION	96
3.2483-3.3531	0.2574	140	0.2016	2811	X-RAY DIFFRACTION	98
3.3531-3.473	0.2321	121	0.2057	2798	X-RAY DIFFRACTION	97
3.473-3.612	0.2917	150	0.196	2762	X-RAY DIFFRACTION	98
3.612-3.7764	0.2648	154	0.1882	2822	X-RAY DIFFRACTION	98
3.7764-3.9755	0.2311	184	0.178	2717	X-RAY DIFFRACTION	97
3.9755-4.2245	0.24	108	0.1658	2733	X-RAY DIFFRACTION	95
4.2245-4.5506	0.2357	149	0.1549	2793	X-RAY DIFFRACTION	98
4.5506-5.0084	0.2244	152	0.1585	2821	X-RAY DIFFRACTION	98
5.0084-5.7328	0.2146	168	0.1656	2816	X-RAY DIFFRACTION	98
5.7328-7.2212	0.2312	157	0.1783	2685	X-RAY DIFFRACTION	95
7.2212-65.2618	0.1298	151	0.1274	2754	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	2.1082	-0.0294	1.6557	2.5068	-0.2749	3.4812	-0.1049	0.2677	0.0203	-0.205	-0.1183	-0.9273	0.0131	0.1549	0.2221	0.317	-0.0306	0.039	0.3618	-0.0282	0.8031	4.9984	-14.7954	-70.3869
2	1.588	-0.8581	0.6157	2.5973	0.4992	1.7169	-0.1616	0.2394	0.8832	-0.3719	-0.3092	0.2561	-0.487	-0.1172	0.4307	0.436	0.0614	-0.2048	0.4443	-0.0219	0.9429	-12.3742	2.4265	-69.6552
3	2.3388	-1.7264	-0.1598	3.4117	-0.4128	2.7355	-0.2681	-0.2913	0.0248	0.6046	-0.0466	-0.2185	-0.2307	-0.0261	0.3011	0.4425	0.0312	-0.1936	0.3689	-0.0772	0.8293	1.5059	-15.4654	-44.6368
4	4.6288	-0.6539	0.2122	3.3789	-0.6247	2.1958	-0.3476	-0.4303	0.4917	-0.0598	0.2346	0.2234	0.2643	-0.8432	0.0727	0.2914	-0.1118	0.014	0.7628	-0.2432	0.5531	-30.4076	-19.8414	-64.356
5	3.9025	0.0244	0.0788	2.7897	0.6211	2.7936	0.0455	-0.1121	-0.3714	0.6297	0.112	-0.5278	0.2476	0.5192	-0.1405	0.708	0.129	-0.2027	0.5482	-0.0318	0.6127	-28.0172	-9.1604	3.4294
6	3.9625	-0.6199	-0.8432	4.1513	-0.2298	4.9194	0.3458	-0.2881	0.4549	0.2798	-0.0462	-0.5899	-0.7506	0.6553	-0.3269	0.6547	-0.0818	-0.02	0.5032	-0.0817	0.6462	-25.7126	7.7163	-14.4041
7	3.139	0.5128	-0.0954	4.7376	-0.5275	3.1083	0.0741	0.002	-0.043	-0.06	0.0058	0.4486	0.2571	-0.4531	-0.1121	0.6473	0.0018	0.0248	0.4834	0.0336	0.4442	-52.7596	-9.9954	-4.5267
8	2.4694	-0.6778	-0.3858	5.2787	-0.9822	4.8537	0.0125	0.1689	-0.3103	0.1485	-0.1373	-0.2054	0.4644	0.5426	0.1466	0.485	0.1739	-0.0322	0.5917	-0.0742	0.5315	-27.6299	-15.8504	-32.4124
9	2.8656	0.967	0.5236	2.7439	-1.7225	1.1987	-0.1843	-0.5292	-0.2862	-0.0932	-0.1182	-0.1424	0.2505	-0.362	0.2503	0.3762	-0.0086	0.0869	0.6018	-0.1027	0.7178	-18.3438	-25.1636	-52.8414
10	1.331	2.005	0.8457	5.017	1.9535	0.7368	0.1771	-0.1673	-0.2112	0.0036	-0.2603	-0.1489	0.1382	-0.3915	0.0311	0.7396	-0.0209	-0.0999	0.6123	-0.066	0.6768	-42.4829	-20.94	-23.9285

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 860 through 873 ) or chain 'G' and (resid 838 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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