PDB-5yuw: DNA polymerase IV - DNA ternary complex 6

ID or keywords:

Entry

Database: PDB / ID: 5yuw

Title

DNA polymerase IV - DNA ternary complex 6

Components

DNA polymerase IV
DTN1
DTN2C

Keywords

DNA BINDING PROTEIN/DAN /

DNA POLYMERASE /

DNA BINDING PROTEIN / DNA BINDING PROTEIN-DAN 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: 2.124 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	Nov 7, 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.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_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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Download

PDBx/mmCIF format	5yuw.cif.gz	369.4 KB	Display	PDBx/mmCIF format
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Validation report

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

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Related structure data

Related structure data	5yurC 5yusC 5yutC 5yuuC 5yuvC 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	5yus-2 5yv1-2 4irc-2 5yur-2 5c5j-2 4q43-1 5yuy-2 5yv2-2 5yuu-2 4q44-1 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

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Deposited unit

A: DNA polymerase IV

B: DTN1

C: DTN2C

F: DNA polymerase IV

G: DTN1

H: DTN2C

hetero molecules

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

1

A: DNA polymerase IV

B: DTN1

C: DTN2C

hetero molecules

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

2

F: DNA polymerase IV

G: DTN1

H: DTN2C

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.190, 57.010, 110.040
Angle α, β, γ (deg.)	90.00, 94.59, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AF

#1: Protein	DNA polymerase IV / / Pol IV / Translesion synthesis polymerase IV / TSL polymerase IV Mass: 39589.895 Da / Num. of mol.: 2 / Fragment: UNP residues 2-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: dinB / Production host: Escherichia coli (E. coli) / References: UniProt: Q47155, DNA-directed DNA polymerase

#1: Protein

DNA polymerase IV /

/ Pol IV / Translesion synthesis polymerase IV / TSL polymerase IV

Mass: 39589.895 Da / Num. of mol.: 2 / Fragment: UNP residues 2-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: dinB / Production host:

Escherichia coli (E. coli) / References: UniProt: Q47155,

DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules BGCH

#2: DNA chain	DTN1 Mass: 5492.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain	DTN2C Mass: 5796.747 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: PVI represents the pentacovalent intermediate formed during DNA synthesis Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 3 types, 529 molecules

#4: Chemical	ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate Mass: 482.168 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₂O₁₄P₃
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.77 Å³/Da / Density % sol: 55.6 %
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 / Serial crystal experiment: N
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: 2.124→109.7 Å / Num. obs: 60569 / % possible obs: 99.8 % / Redundancy: 3.8 % / R_merge(I) obs: 0.039 / Net I/σ(I): 12.2
Reflection shell	Resolution: 2.124→2.14 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.549 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7

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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: 2.124→44.64 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 25.67

	R_factor	Num. reflection	% reflection
R_free	0.232	5810	5.08 %
R_work	0.189	-	-
obs	0.191	59515	97.1 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.124→44.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5373	1322	91	522	7308

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7076
X-RAY DIFFRACTION	f_angle_d	1.632	9857
X-RAY DIFFRACTION	f_dihedral_angle_d	22.976	4135
X-RAY DIFFRACTION	f_chiral_restr	0.057	1091
X-RAY DIFFRACTION	f_plane_restr	0.006	1032

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 (%)
2.124-2.1481	0.348	203	0.2725	3354	X-RAY DIFFRACTION	90
2.1481-2.1734	0.3198	158	0.2709	3457	X-RAY DIFFRACTION	91
2.1734-2.1999	0.2897	217	0.2702	3390	X-RAY DIFFRACTION	91
2.1999-2.2278	0.3379	171	0.2818	3391	X-RAY DIFFRACTION	92
2.2278-2.2571	0.3217	182	0.3176	3423	X-RAY DIFFRACTION	92
2.2571-2.288	0.2743	157	0.2693	3521	X-RAY DIFFRACTION	93
2.288-2.3207	0.297	191	0.2467	3394	X-RAY DIFFRACTION	93
2.3207-2.3553	0.2876	217	0.2464	3577	X-RAY DIFFRACTION	95
2.3553-2.3921	0.2988	190	0.2455	3587	X-RAY DIFFRACTION	95
2.3921-2.4313	0.2806	185	0.2446	3495	X-RAY DIFFRACTION	95
2.4313-2.4733	0.2877	192	0.2359	3601	X-RAY DIFFRACTION	96
2.4733-2.5182	0.2846	187	0.2342	3600	X-RAY DIFFRACTION	97
2.5182-2.5667	0.2853	192	0.2356	3568	X-RAY DIFFRACTION	97
2.5667-2.619	0.3402	208	0.2381	3644	X-RAY DIFFRACTION	98
2.619-2.676	0.2748	198	0.2347	3702	X-RAY DIFFRACTION	99
2.676-2.7382	0.2932	207	0.231	3702	X-RAY DIFFRACTION	99
2.7382-2.8067	0.2655	234	0.2105	3678	X-RAY DIFFRACTION	100
2.8067-2.8826	0.2238	183	0.213	3764	X-RAY DIFFRACTION	100
2.8826-2.9674	0.2631	173	0.2054	3718	X-RAY DIFFRACTION	100
2.9674-3.0631	0.2757	199	0.202	3697	X-RAY DIFFRACTION	100
3.0631-3.1726	0.2426	196	0.1885	3799	X-RAY DIFFRACTION	100
3.1726-3.2996	0.2423	171	0.1757	3704	X-RAY DIFFRACTION	100
3.2996-3.4497	0.1766	162	0.1667	3783	X-RAY DIFFRACTION	100
3.4497-3.6315	0.1967	216	0.1748	3699	X-RAY DIFFRACTION	100
3.6315-3.8589	0.244	204	0.1668	3714	X-RAY DIFFRACTION	100
3.8589-4.1566	0.2042	201	0.152	3734	X-RAY DIFFRACTION	100
4.1566-4.5745	0.2071	185	0.1449	3742	X-RAY DIFFRACTION	100
4.5745-5.2356	0.1887	208	0.1494	3714	X-RAY DIFFRACTION	100
5.2356-6.5929	0.1957	212	0.1699	3720	X-RAY DIFFRACTION	100
6.5929-44.6458	0.1448	211	0.1465	3684	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	1.3302	-0.5694	0.6936	2.3499	-0.2882	2.42	-0.0061	0.2129	-0.0734	-0.392	0.0201	-0.6638	0.1467	0.1165	0.0475	0.2262	-0.0233	0.0876	0.2363	-0.0288	0.4747	4.6954	-13.8079	-69.9461
2	1.5004	-0.2988	0.541	2.9559	0.037	1.4525	-0.1079	0.1933	0.5937	-0.3356	-0.1447	0.0969	-0.2714	-0.1844	0.1875	0.2616	0.0138	-0.089	0.2237	0.0105	0.4786	-12.631	3.4132	-69.187
3	2.1161	-0.784	0.25	1.9929	-0.1691	1.8341	-0.2602	-0.3374	0.063	0.5232	0.0086	-0.2781	-0.1618	-0.0678	0.1877	0.3056	0.0364	-0.093	0.2421	-0.0528	0.4978	1.3053	-14.5693	-44.3531
4	3.1267	0.263	0.543	3.3232	-0.3068	2.4576	-0.1451	-0.348	0.4381	-0.2212	0.1677	0.2273	0.2581	-0.4733	-0.096	0.1585	-0.0629	0.0218	0.467	-0.1329	0.3222	-30.7106	-18.8424	-63.9615
5	1.8523	0.3191	-0.0716	1.5571	0.2032	1.2694	0.0657	-0.1713	-0.1738	0.4041	-0.0217	-0.3043	0.263	0.3109	-0.063	0.5552	0.0776	-0.0999	0.3903	0.0088	0.2946	-27.9141	-8.0645	3.3084
6	1.3942	0.0654	-0.4781	2.4421	-0.3993	1.4448	0.1919	0.0075	0.2007	0.081	-0.0699	-0.2105	-0.6186	0.4803	-0.0697	0.5919	-0.0443	0.0164	0.3941	-0.0523	0.3205	-25.5824	8.7919	-14.5692
7	1.72	0.0199	0.1515	1.9557	-0.7004	1.0041	0.0359	0.0219	0.0713	-0.0669	0.0432	0.2846	0.0689	-0.1753	-0.0882	0.567	-0.0104	0.0396	0.3842	0.0173	0.2603	-52.6404	-8.8571	-4.5283
8	1.9197	0.1122	-0.327	2.2106	0.5504	3.184	-0.0979	0.0455	-0.1895	0.148	-0.0593	-0.0884	0.3916	0.3739	0.1388	0.4119	0.1365	0.0352	0.4122	-0.0062	0.2335	-27.6851	-14.756	-32.4493
9	4.0814	0.9594	-0.0361	2.1686	-0.7481	1.5119	-0.0538	-0.6187	-0.5123	0.1157	-0.1434	-0.1562	0.1678	-0.2032	0.0843	0.2272	-0.0093	0.0716	0.3484	-0.0149	0.3524	-18.5258	-24.0159	-52.7664
10	0.9818	1.3854	0.6012	2.0714	0.941	0.3915	0.1091	-0.0438	-0.0352	0.1224	-0.1436	0.0427	0.1072	-0.2395	-0.0197	0.6062	-0.011	-0.0091	0.4299	-0.0415	0.2929	-41.8759	-19.2852	-23.0962

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 901 THROUGH 902)
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 838 THROUGH 854 ) OR CHAIN 'C' AND (RESID 857 THROUGH 873) OR CHAIN 'A' AND (RESID 900 THROUGH 902)

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Protein , 1 types, 2 molecules AF

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DNA chain , 2 types, 4 molecules BGCH

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Non-polymers , 3 types, 529 molecules

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-Protein , 1 types, 2 molecules AF

-DNA chain , 2 types, 4 molecules BGCH

-Non-polymers , 3 types, 529 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

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+About Yorodumi

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

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+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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This page

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This web site

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Open data

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Validation report

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Related structure data

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Assembly

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Components

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Protein , 1 types, 2 molecules AF

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DNA chain , 2 types, 4 molecules BGCH

-
Non-polymers , 3 types, 529 molecules

-
Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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

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

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Yorodumi