PDB-4ds5: Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA ...

ID or keywords:

Entry

Database: PDB / ID: 4ds5

Title

Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and rCTP in presence of Mg2+

Components

DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*C)-3')
DNA polymerase

Keywords

Transferase/DNA / DNA Polymerase I / Transferase-DNA complex

Function / homology

Function and homology information

5'-3' exonuclease activity / 3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function

Biological species

Geobacillus kaustophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.68 Å

Authors

Wang, W. / Beese, L.S.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides.
Authors: Wang, W. / Wu, E.Y. / Hellinga, H.W. / Beese, L.S.

History

Deposition	Feb 17, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 6, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 13, 2012	Group: Database references
Revision 1.2	Nov 21, 2012	Group: Database references
Revision 1.3	Sep 13, 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_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ds5.cif.gz	748.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ds5.ent.gz	623.6 KB	Display	PDB format
PDBx/mmJSON format	4ds5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ds5_validation.pdf.gz	474.5 KB	Display	wwPDB validaton report
Full document	4ds5_full_validation.pdf.gz	488 KB	Display
Data in XML	4ds5_validation.xml.gz	53.6 KB	Display
Data in CIF	4ds5_validation.cif.gz	81.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ds/4ds5 ftp://data.pdbj.org/pub/pdb/validation_reports/ds/4ds5	HTTPS FTP

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Related structure data

Related structure data	4dqiC 4dqpC 4dqqC 4dqrC 4dqsC 4ds4SC 4dseC 4dsfC 4e0dC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4f4k-1 4f3o-1 4f3o-2 1lv5-2 4ds4-1 4f8r-1 4e0d-d 4bdp-d 4dsi-d 4ez6-2 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

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similarity (1)
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Deposited unit

A: DNA polymerase

D: DNA polymerase

B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*C)-3')

C: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')

E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*C)-3')

F: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')

hetero molecules

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

1

A: DNA polymerase

B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*C)-3')

C: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')

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

2

D: DNA polymerase

E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*C)-3')

F: DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')

hetero molecules

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

Unit cell

Length a, b, c (Å)	93.880, 108.860, 150.960
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	DNA polymerase Mass: 67474.289 Da / Num. of mol.: 2 / Fragment: unp residues 287-878 / Mutation: D598A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: polA, GK2730 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q5KWC1, DNA-directed DNA polymerase
#2: DNA chain	DNA (5'-D(CPCPTPGPAPCPTPCPC)-3') Mass: 2651.750 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details*: DNA Primer Strand
#3: DNA chain	DNA (5'-D(CPAPTPGPGPGPAPGPTPCPAPGPG)-3') Mass: 4056.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details*: DNA Template Strand
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1118 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS ...AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS NOT AVAILABLE IN THE UNIPROT DATABASE. IT DIFFERS FROM UNP Q5KWC1 BY THIS SINGLE RESIDUE

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.7 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 50% Saturated Ammonium Sulfate, 2.5% MPD, 10mM MgSO4, 100mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 12.3.1 / Wavelength: 1.1159 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 11, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.1159 Å / Relative weight: 1

Reflection

Resolution: 1.68→100 Å / Num. obs: 157642 / % possible obs: 89.6 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / B_iso Wilson estimate: 31.682 Å² / R_merge(I) obs: 0.062 / Net I/σ(I): 21.08

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.68-1.78	0.466	4.15	1	97.2
1.78-1.9	0.449	6.83	1	91.2
1.9-2.05	0.249	13.12	1	64.1
2.05-2.25	0.155	18.77	1	87.1
2.25-2.52	0.094	26.46	1	86.1
2.52-2.9	0.068	32.33	1	99.1
2.9-3.55	0.049	37.67	1	99.4
3.55-5.02	0.043	40.62	1	98.8
5.02-100	0.034	46.07	1	99.3

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	dev_1026	refinement
PDB_EXTRACT	3.1	data extraction
XDS		data reduction

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: pdb entry 4DS4

4ds4

Resolution: 1.68→54.43 Å / Occupancy max: 1 / Occupancy min: 0.14 / SU ML: 0.16 / σ(F): 2.35 / Phase error: 20.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1989	6639	4.36 %
R_work	0.1758	-	-
obs	0.1768	152367	86.58 %

Solvent computation

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

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.6132 Å²	0 Å²	-0 Å²
2-	-	0.1873 Å²	0 Å²
3-	-	-	-0.8004 Å²

Refinement step

Cycle: LAST / Resolution: 1.68→54.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9145	772	15	1118	11050

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	10285
X-RAY DIFFRACTION	f_angle_d	1.345	14080
X-RAY DIFFRACTION	f_dihedral_angle_d	14.759	3960
X-RAY DIFFRACTION	f_chiral_restr	0.077	1581
X-RAY DIFFRACTION	f_plane_restr	0.007	1698

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 (%)
1.68-1.6991	0.3101	133	0.2488	4874	X-RAY DIFFRACTION	87
1.6991-1.7191	0.2408	240	0.2283	4836	X-RAY DIFFRACTION	88
1.7191-1.74	0.2885	242	0.2221	4897	X-RAY DIFFRACTION	88
1.74-1.7621	0.2579	245	0.2138	4968	X-RAY DIFFRACTION	90
1.7621-1.7853	0.2495	245	0.2085	4978	X-RAY DIFFRACTION	90
1.7853-1.8097	0.2189	260	0.1977	5052	X-RAY DIFFRACTION	91
1.8097-1.8356	0.2186	254	0.1923	5120	X-RAY DIFFRACTION	92
1.8356-1.863	0.2187	251	0.1878	5057	X-RAY DIFFRACTION	92
1.863-1.8921	0.2418	244	0.1889	4868	X-RAY DIFFRACTION	88
1.9231-1.9563	0.2575	72	0.1882	1387	X-RAY DIFFRACTION	81
1.9563-1.9918	0.2335	237	0.1851	5122	X-RAY DIFFRACTION	92
1.9918-2.0302	0.2018	197	0.1771	5404	X-RAY DIFFRACTION	96
2.0302-2.0716	0.1904	196	0.1687	5418	X-RAY DIFFRACTION	96
2.0716-2.1166	0.1835	219	0.1702	5464	X-RAY DIFFRACTION	97
2.1166-2.1659	0.181	223	0.1677	5444	X-RAY DIFFRACTION	97
2.1659-2.2201	0.2101	244	0.1699	5368	X-RAY DIFFRACTION	95
2.2201-2.2801	0.1622	18	0.1875	367	X-RAY DIFFRACTION	7
2.2801-2.3472	0.1805	204	0.1651	5440	X-RAY DIFFRACTION	97
2.3472-2.4229	0.2104	229	0.1605	5549	X-RAY DIFFRACTION	98
2.4229-2.5095	0.1918	224	0.1692	5543	X-RAY DIFFRACTION	98
2.5095-2.61	0.1646	236	0.1743	5544	X-RAY DIFFRACTION	98
2.61-2.7288	0.1995	241	0.1797	5557	X-RAY DIFFRACTION	99
2.7288-2.8726	0.2292	256	0.1899	5579	X-RAY DIFFRACTION	99
2.8726-3.0526	0.225	270	0.1861	5553	X-RAY DIFFRACTION	99
3.0526-3.2883	0.1804	289	0.1757	5591	X-RAY DIFFRACTION	99
3.2883-3.6191	0.1742	290	0.1619	5598	X-RAY DIFFRACTION	99
3.6191-4.1427	0.1769	278	0.1578	5542	X-RAY DIFFRACTION	98
4.1427-5.2187	0.1907	300	0.1507	5715	X-RAY DIFFRACTION	100
5.2187-54.4586	0.2073	302	0.2012	5893	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	1.8554	0.4168	-0.0756	2.2178	0.6286	2.1054	0.052	0.3617	-0.456	0.2805	0.0083	-0.024	1.092	0.0927	-0.0497	0.7302	0.0805	0.021	0.346	-0.0448	0.3796	116.655	-64.2489	23.6756
2	2.3621	1.3567	0.0464	2.6922	0.3846	1.6733	-0.0672	0.53	-0.1374	0.0917	0.178	0.1552	0.4355	0.2674	-0.0971	0.4409	0.1042	0.0345	0.3552	0.0196	0.2482	118.2513	-53.088	21.9862
3	0.5104	-0.0948	0.0353	1.7624	-0.3458	2.0474	-0.0847	-0.1622	0.0897	0.5219	0.1014	0.3038	-0.0936	0.0243	-0.0191	0.3656	-0.0408	0.0326	0.2247	-0.0063	0.3042	109.8564	-29.7678	48.1728
4	1.3476	0.1306	-0.1281	1.5307	0.3526	1.0306	-0.0534	-0.2542	0.0988	0.3382	0.0921	-0.2253	0.0865	0.7511	0.0112	0.3463	-0.0201	-0.047	0.502	0.0142	0.2284	128.1412	-32.579	42.4459
5	3.0134	-0.0615	2.0157	1.4685	-0.3322	1.4272	-0.1899	-1.1592	0.543	0.4458	0.2218	-0.3138	-0.7075	0.2584	-0.0121	0.6144	-0.1248	-0.0307	0.7909	-0.189	0.4659	129.6952	-9.2388	40.2568
6	0.9076	0.4992	-0.6981	1.2315	0.2834	2.3336	-0.032	-0.1833	-0.0109	0.1777	-0.0244	-0.3328	0.0308	0.8103	0.0844	0.2276	0.0008	-0.0333	0.5408	0.0264	0.2605	131.9091	-32.2542	34.5908
7	1.7793	-0.4492	0.3515	1.8807	0.7087	1.5095	0.0657	0.0018	-0.1997	-0.1064	0.0297	-0.0895	0.1501	0.1035	-0.0514	0.1092	0.0221	-0.0107	0.0843	-0.0182	0.1215	137.9977	-47.7549	-9.4145
8	0.6716	0.4578	-0.4255	1.2709	-0.4199	0.4847	-0.1138	0.2808	0.2098	-0.4363	0.2478	0.1149	-0.0697	-0.1966	-0.1105	0.3134	-0.0324	-0.0257	0.2226	0.0402	0.1818	123.2682	-17.8501	-30.9363
9	1.2832	-0.1763	-0.1125	1.2985	0.644	1.3184	0.0482	0.1273	0.2386	-0.1815	-0.0629	0.0305	-0.1832	-0.0589	0.0255	0.0746	0.0075	0.0038	0.0936	0.0212	0.1263	118.8224	-20.5129	-9.525
10	6.2277	-0.778	0.119	1.8954	-0.6451	3.758	-0.5522	0.0545	0.3488	-0.3671	0.2661	0.3723	-0.2063	0.0255	0.2655	0.3728	-0.0309	-0.0402	0.1811	-0.0333	0.3411	108.5081	-28.0504	40.2105
11	1.3939	-0.7641	-0.0505	1.6642	0.8148	1.3448	0.0366	0.0071	0.4848	-0.1868	0.0373	0.6351	-0.0971	-0.0698	-0.1001	0.2885	-0.0136	-0.0009	0.2293	0.0402	0.4053	109.8265	-28.006	38.0272
12	2.7466	1.4435	-1.5626	1.0083	-0.6415	4.4977	-0.0008	0.3541	0.45	-0.2109	0.1781	-0.3701	-0.0157	-0.0614	-0.2086	0.2895	0.0467	0.0572	0.1886	0.0395	0.3177	129.8093	-18.4848	-27.212
13	1.0402	-0.0241	-0.5574	0.7044	-1.0796	1.9917	0.0863	0.2452	0.1393	-0.5523	0.0954	-0.3287	-0.3519	0.0775	-0.2746	0.2872	-0.0269	0.0851	0.2332	0.0051	0.1914	130.5538	-21.3903	-26.5303

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 297:354)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 355:467)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 468:604)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 605:676)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 677:743)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 744:876)
7	X-RAY DIFFRACTION	7	chain 'D' and (resseq 296:467)
8	X-RAY DIFFRACTION	8	chain 'D' and (resseq 468:586)
9	X-RAY DIFFRACTION	9	chain 'D' and (resseq 587:876)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 21:29)
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 2:12)
12	X-RAY DIFFRACTION	12	chain 'E' and (resseq 21:29)
13	X-RAY DIFFRACTION	13	chain 'F' and (resseq 1:12)

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