PDB-4ds4: Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA ...

ID or keywords:

Entry

Database: PDB / ID: 4ds4

Title

Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and rCTP in presence of Mn2+

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*(DOC))-3')
DNA polymerase

Keywords

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

Function / homology

Function and homology information

double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / 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: 1.681 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_conn / 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_conn.pdbx_leaving_atom_flag / _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	4ds4.cif.gz	747.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4ds4.ent.gz	622.5 KB	Display	PDB format
PDBx/mmJSON format	4ds4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ds4_validation.pdf.gz	476.3 KB	Display	wwPDB validaton report
Full document	4ds4_full_validation.pdf.gz	487.7 KB	Display
Data in XML	4ds4_validation.xml.gz	52.6 KB	Display
Data in CIF	4ds4_validation.cif.gz	80.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ds/4ds4 ftp://data.pdbj.org/pub/pdb/validation_reports/ds/4ds4	HTTPS FTP

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Related structure data

Related structure data	4dqiC 4dqpC 4dqqC 4dqrC 4dqsC 4ds5C 4dseC 4dsfC 4e0dC 2hviS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4yfu-1 4f8r-1 4f3o-2 4dsf-2 6us5-2 4dsi-d 4ds5-1 4f2s-1 4bdp-d 2hvi-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

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Deposited unit

A: DNA polymerase

D: DNA polymerase

B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-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*(DOC))-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*(DOC))-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*(DOC))-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)	93.790, 108.770, 150.710
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(CPCPTPGPAPCPTPCP(DOC))-3') Mass: 2635.751 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.: 1082 / 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: 2.59 Å³/Da / Density % sol: 52.53 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 50% Saturated Ammonium Sulfate, 2.5% MPD, 10mM MnSO4, 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: 1.1158 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: 1.1158 Å / Relative weight: 1

Reflection

Resolution: 1.68→100 Å / Num. obs: 159378 / % possible obs: 90.9 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / B_iso Wilson estimate: 32.922 Å² / R_merge(I) obs: 0.067 / Net I/σ(I): 21.41

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.68-1.78	0.48	3.95	1	94.4
1.78-1.91	0.297	6.32	1	85.6
1.91-2.06	0.3	12.5	1	75.8
2.06-2.25	0.19	17.95	1	89.4
2.25-2.52	0.114	25.73	1	89.5
2.52-2.91	0.08	32.78	1	100
2.91-3.56	0.056	39.83	1	100
3.56-5.01	0.047	44.57	1	99.5
5.01-100	0.039	49.34	1	99.7

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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 2HVI

2hvi

Resolution: 1.681→64.252 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.16 / σ(F): 2.35 / Phase error: 19.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1986	6888	4.49 %
R_work	0.1739	-	-
obs	0.175	153529	87.72 %

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-	-1.7178 Å²	0 Å²	0 Å²
2-	-	1.629 Å²	-0 Å²
3-	-	-	0.0888 Å²

Refinement step

Cycle: LAST / Resolution: 1.681→64.252 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9145	772	15	1082	11014

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	10285
X-RAY DIFFRACTION	f_angle_d	1.342	14080
X-RAY DIFFRACTION	f_dihedral_angle_d	14.681	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 (%)
1.6811-1.7002	0.2756	194	0.2423	3698	X-RAY DIFFRACTION	68
1.7002-1.7202	0.2561	262	0.2231	4973	X-RAY DIFFRACTION	90
1.7202-1.7412	0.2786	261	0.2139	4951	X-RAY DIFFRACTION	91
1.7412-1.7632	0.2636	265	0.2094	5037	X-RAY DIFFRACTION	92
1.7632-1.7864	0.245	266	0.2055	5067	X-RAY DIFFRACTION	92
1.7864-1.8109	0.2448	271	0.1947	5148	X-RAY DIFFRACTION	93
1.8109-1.8368	0.2191	268	0.1923	5091	X-RAY DIFFRACTION	93
1.8368-1.8642	0.2259	267	0.1866	5068	X-RAY DIFFRACTION	93
1.8642-1.8933	0.2436	230	0.1914	4372	X-RAY DIFFRACTION	89
1.9244-1.9576	0.231	122	0.1918	2318	X-RAY DIFFRACTION	71
1.9576-1.9932	0.2359	233	0.1854	5304	X-RAY DIFFRACTION	96
1.9932-2.0315	0.189	204	0.1741	5433	X-RAY DIFFRACTION	98
2.0315-2.073	0.1928	203	0.1711	5503	X-RAY DIFFRACTION	98
2.073-2.1181	0.1765	216	0.1674	5512	X-RAY DIFFRACTION	98
2.1181-2.1673	0.2052	220	0.1684	5523	X-RAY DIFFRACTION	99
2.1673-2.2215	0.1926	250	0.169	5299	X-RAY DIFFRACTION	96
2.2215-2.2816	0.2001	38	0.1944	1077	X-RAY DIFFRACTION	19
2.2816-2.3487	0.1793	209	0.162	5496	X-RAY DIFFRACTION	99
2.3487-2.4246	0.2104	229	0.1636	5547	X-RAY DIFFRACTION	99
2.4246-2.5112	0.1899	222	0.1694	5590	X-RAY DIFFRACTION	99
2.5112-2.6118	0.1802	235	0.1732	5583	X-RAY DIFFRACTION	99
2.6118-2.7306	0.2224	244	0.1811	5544	X-RAY DIFFRACTION	99
2.7306-2.8746	0.211	253	0.1847	5577	X-RAY DIFFRACTION	100
2.8746-3.0547	0.2113	268	0.184	5584	X-RAY DIFFRACTION	100
3.0547-3.2905	0.1953	290	0.1743	5583	X-RAY DIFFRACTION	100
3.2905-3.6216	0.1719	286	0.1586	5598	X-RAY DIFFRACTION	99
3.6216-4.1456	0.173	283	0.154	5580	X-RAY DIFFRACTION	99
4.1456-5.2227	0.1869	296	0.1507	5701	X-RAY DIFFRACTION	100
5.2227-64.2986	0.2046	303	0.1986	5884	X-RAY DIFFRACTION	100

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	2.2513	0.4971	-0.3056	2.9337	0.5586	2.7052	-0.048	0.3189	-0.5011	0.1358	0.0726	-0.2339	0.757	0.1022	-0.0118	0.553	0.0826	-0.0039	0.3195	-0.0337	0.3838	118.9689	-63.8174	24.2916
2	2.2742	1.2748	-0.0641	2.8561	0.5284	1.7344	-0.0813	0.499	-0.0187	-0.1761	0.1463	0.265	0.2286	0.0976	-0.0807	0.3768	0.0548	0.003	0.3276	0.0318	0.2563	116.4535	-51.1976	21.0532
3	0.7572	-0.2383	-0.0803	1.6604	-0.3307	1.9575	-0.0817	-0.1774	0.089	0.4267	0.1188	0.2633	-0.1352	0.0045	-0.0355	0.3287	-0.048	-0.0015	0.2112	0.005	0.276	109.7434	-29.777	48.1311
4	1.5217	0.1506	0.0118	1.4831	0.2755	1.432	-0.0403	-0.2477	0.0645	0.2683	0.0476	-0.2356	0.0281	0.6258	0.0194	0.3251	-0.0297	-0.057	0.4423	0.0323	0.2373	128.0248	-32.612	42.425
5	1.6754	-0.7128	0.128	2.1943	-0.2149	1.3851	-0.0979	-0.5134	0.423	0.2198	0.1304	-0.2501	-0.5336	0.2266	-0.0443	0.3957	-0.1226	-0.008	0.572	-0.0658	0.3403	128.6809	-14.0713	32.6188
6	1.0262	0.4545	-0.1429	1.1997	0.0432	2.441	0.0124	-0.1716	-0.0909	0.2952	-0.1387	-0.4713	0.097	0.8863	0.1073	0.2897	0.0254	-0.0623	0.5863	0.0667	0.307	133.6567	-36.1935	40.6423
7	1.779	-0.2749	0.3181	1.8488	0.6851	1.6619	0.0377	0.0187	-0.144	-0.0727	0.0252	-0.0987	0.1444	0.1111	-0.0364	0.111	0.0231	-0.005	0.0927	-0.0182	0.1065	137.8935	-47.6746	-9.4073
8	0.6867	0.3931	-0.3183	1.4097	-0.5211	0.6239	-0.1153	0.2692	0.1807	-0.4241	0.2389	0.0769	-0.0683	-0.2078	-0.1158	0.3059	-0.0232	-0.007	0.2215	0.0213	0.1787	123.1445	-17.8349	-30.9255
9	1.1952	-0.0451	-0.122	1.2848	0.6034	1.2986	0.0491	0.1215	0.2018	-0.1506	-0.049	0.0381	-0.1688	-0.0551	0.0189	0.083	0.0128	0.0049	0.1024	0.0234	0.124	118.6981	-20.4883	-9.5253
10	5.6185	-0.5356	0.3479	2.1609	-0.3162	3.8537	-0.5217	0.1021	0.2443	-0.4763	0.2313	0.5317	-0.2903	0.077	0.2602	0.3743	-0.038	-0.076	0.188	-0.0181	0.3663	108.4118	-28.0449	40.1308
11	1.5751	-0.0174	-0.3223	2.1918	0.5888	1.4498	0.0775	0.124	0.5393	-0.2356	0.0668	0.6353	-0.2122	-0.1624	-0.1396	0.3074	0.0045	-0.0196	0.2267	0.0582	0.3824	109.7234	-28.0053	37.96
12	2.2215	1.5601	-1.2417	1.2224	-0.7636	4.0596	-0.07	0.2068	0.2482	-0.2189	0.1204	-0.4237	0.0067	0.0797	-0.0786	0.3011	0.0589	0.0548	0.2072	0.0221	0.3318	129.6722	-18.4431	-27.1768
13	1.1485	-0.3061	-0.6549	0.5203	-0.7074	2.1774	0.0718	0.2858	0.0565	-0.5217	0.0982	-0.3638	-0.2272	0.1333	-0.2081	0.2747	-0.0397	0.0946	0.2247	-0.0096	0.1828	130.4169	-21.3546	-26.5024

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 297:372)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 373:467)
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 677:780)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 781:876)
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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About Yorodumi

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Yorodumi