PDB-4exw: The structure of DdrB from Deinococcus: a new fold for single-str...

ID or keywords:

Entry

Database: PDB / ID: 4exw

Title

The structure of DdrB from Deinococcus: a new fold for single-stranded DNA binding proteins.

Components

Single-stranded DNA-binding protein DdrB

Keywords

DNA BINDING PROTEIN / Anti-parallel beta-barrel / pentamer / DNA binding / DNA annealing

Function / homology

Single-stranded DNA binding protein DdrB-like / DdrB-like protein / single-stranded DNA binding / DNA repair / Single-stranded DNA-binding protein DdrB

Function and homology information

Biological species

Deinococcus geothermalis DSM 11300 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.8 Å

Authors

Sugiman-Marangos, S. / Junop, M.S.

Citation

Journal: Nucleic Acids Res. / Year: 2010
Title: The structure of DdrB from Deinococcus: a new fold for single-stranded DNA binding proteins.
Authors: Sugiman-Marangos, S. / Junop, M.S.

History

Deposition	May 1, 2012	Deposition site: RCSB / Processing site: RCSB
Supersession	Jul 11, 2012	ID: 3KDV
Revision 1.0	Jul 11, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 10, 2018	Group: Data collection / Database references / Structure summary Category: citation / entity Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4exw.cif.gz	250.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4exw.ent.gz	211.2 KB	Display	PDB format
PDBx/mmJSON format	4exw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4exw_validation.pdf.gz	460.8 KB	Display	wwPDB validaton report
Full document	4exw_full_validation.pdf.gz	463.2 KB	Display
Data in XML	4exw_validation.xml.gz	22.2 KB	Display
Data in CIF	4exw_validation.cif.gz	30.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ex/4exw ftp://data.pdbj.org/pub/pdb/validation_reports/ex/4exw	HTTPS FTP

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Related structure data

Similar structure data	4mlw-2 4hqb-d 1uo9-1 1dcs-1 2a48-1 2b3y-2 6nqr-1 6nqr-2 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

Deposited unit

A: Single-stranded DNA-binding protein DdrB

B: Single-stranded DNA-binding protein DdrB

C: Single-stranded DNA-binding protein DdrB

D: Single-stranded DNA-binding protein DdrB

E: Single-stranded DNA-binding protein DdrB

103 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	102.872, 102.872, 96.731
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Single-stranded DNA-binding protein DdrB / DNA damage response protein B Mass: 20637.402 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus geothermalis DSM 11300 (bacteria) Strain: DSM11300 / Gene: ddrB, Dgeo_0295 / Plasmid: pET151-D-topo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1J1N6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Single-stranded DNA-binding protein DdrB / DNA damage response protein B

Mass: 20637.402 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Deinococcus geothermalis DSM 11300 (bacteria)
Strain: DSM11300 / Gene: ddrB, Dgeo_0295 / Plasmid: pET151-D-topo / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1J1N6

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.86 Å³/Da / Density % sol: 56.99 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Sodium acetate anhydrous, 2.45 M Ammonium sulfate, 0.01 M Praseodymium(III) acetate hydrate., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9798 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2009
Radiation	Monochromator: Si(111)crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9798 Å / Relative weight: 1
Reflection	Resolution: 2.8→50 Å / Num. all: 28588 / Num. obs: 27742 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / B_iso Wilson estimate: 89.787 Å² / R_merge(I) obs: 0.096
Reflection shell	Resolution: 2.8→2.86 Å / Redundancy: 10.8 % / R_merge(I) obs: 0.423 / Mean I/σ(I) obs: 6.67 / Num. unique all: 1590 / % possible all: 100

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Processing

Software

Name	Version	Classification
CBASS		data collection
SOLVE		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.8→35.235 Å / SU ML: 0.4 / σ(F): 1.96 / Phase error: 26.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2544	3734	6.73 %	Random
R_work	0.2311	-	-	-
all	0.2327	55470	-	-
obs	0.2327	55470	98.39 %	-

Solvent computation

Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 75.236 Å² / k_sol: 0.27 e/Å³

Displacement parameters

B_iso mean: 92.74 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.5506 Å²	0 Å²	0 Å²
2-	-	-6.5506 Å²	0 Å²
3-	-	-	13.1012 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→35.235 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4535	0	0	68	4603

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4643
X-RAY DIFFRACTION	f_angle_d	0.768	6300
X-RAY DIFFRACTION	f_dihedral_angle_d	14.223	1586
X-RAY DIFFRACTION	f_chiral_restr	0.05	676
X-RAY DIFFRACTION	f_plane_restr	0.004	817

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 (%)
2.8001-2.8355	0.4348	146	0.3437	1912	X-RAY DIFFRACTION	98
2.8355-2.8728	0.3275	140	0.3314	1912	X-RAY DIFFRACTION	99
2.8728-2.9122	0.2994	138	0.3181	1886	X-RAY DIFFRACTION	98
2.9122-2.9537	0.3468	134	0.3044	1960	X-RAY DIFFRACTION	99
2.9537-2.9978	0.4442	130	0.2911	1932	X-RAY DIFFRACTION	99
2.9978-3.0446	0.2909	142	0.2885	1890	X-RAY DIFFRACTION	99
3.0446-3.0945	0.3008	136	0.2733	1932	X-RAY DIFFRACTION	99
3.0945-3.1478	0.3356	142	0.2822	1946	X-RAY DIFFRACTION	99
3.1478-3.205	0.2962	146	0.2649	1976	X-RAY DIFFRACTION	99
3.205-3.2666	0.2433	118	0.2561	1888	X-RAY DIFFRACTION	99
3.2666-3.3333	0.3046	146	0.2441	1920	X-RAY DIFFRACTION	99
3.3333-3.4057	0.3057	154	0.2584	1912	X-RAY DIFFRACTION	100
3.4057-3.4848	0.246	128	0.2679	1964	X-RAY DIFFRACTION	99
3.4848-3.5719	0.2626	148	0.2606	1814	X-RAY DIFFRACTION	96
3.5719-3.6684	0.3193	118	0.2684	1844	X-RAY DIFFRACTION	92
3.6684-3.7762	0.2976	136	0.2728	1850	X-RAY DIFFRACTION	98
3.7762-3.898	0.2799	146	0.2482	1912	X-RAY DIFFRACTION	98
3.898-4.0371	0.2913	136	0.242	1936	X-RAY DIFFRACTION	98
4.0371-4.1985	0.227	140	0.2085	1836	X-RAY DIFFRACTION	97
4.1985-4.3892	0.2113	140	0.1869	1972	X-RAY DIFFRACTION	99
4.3892-4.6202	0.1798	120	0.168	1962	X-RAY DIFFRACTION	100
4.6202-4.9089	0.2293	138	0.1649	1924	X-RAY DIFFRACTION	100
4.9089-5.2868	0.2231	150	0.1951	1904	X-RAY DIFFRACTION	100
5.2868-5.8167	0.3027	152	0.2029	1946	X-RAY DIFFRACTION	100
5.8167-6.6534	0.1826	148	0.2075	1934	X-RAY DIFFRACTION	100
6.6534-8.3641	0.2297	132	0.2333	1972	X-RAY DIFFRACTION	100
8.3641-35.2379	0.2316	130	0.2478	1900	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	7.0691	1.8479	1.7836	0.6841	0.2982	3.5458	-0.316	0.2944	0.7124	0.047	-0.1664	-0.4256	-0.2084	0.8091	0.4563	0.3002	0.0109	-0.0991	0.4339	0.1281	0.4603	-26.4957	90.4723	-6.3706
2	4.29	2.6572	4.9539	2.1881	3.0117	5.7274	-0.2917	-1.9828	0.2138	0.6947	0.4897	-0.5181	0.1863	0.4024	-0.1757	0.6331	-0.0185	-0.2462	1.4691	-0.1478	0.8385	-12.0579	95.1901	9.6413
3	7.3509	-0.7661	2.7808	3.2041	0.8716	6.0709	-0.0189	-0.7799	-0.2717	0.2957	0.1846	-0.4642	0.1408	1.0336	-1.231	0.3724	-0.0249	-0.2428	1.0974	0.1455	0.5247	-9.8352	89.5566	3.0453
4	2.0014	0.147	4.3193	6.4513	-0.4824	4.4342	0.1292	0.8638	-0.6649	-0.2004	-0.4235	-0.7254	0.3404	1.8675	0.3419	0.2807	0.0641	-0.1993	0.8937	0.1846	0.546	-4.5322	88.8708	-3.2607
5	9.7456	-6.2362	-8.496	3.9921	5.4452	7.4543	-0.8769	-0.8483	-1.8924	1.0938	-0.3672	0.2639	-0.3475	-0.6436	1.5001	1.4562	0.2101	-0.1114	1.0762	0.0157	1.6144	-9.5175	74.0741	4.4163
6	7.408	-0.5534	0.1752	3.6404	-1.2625	6.4936	-0.0738	0.9077	0.3057	-0.3226	-0.6948	-0.3985	0.0958	1.1179	0.5225	0.3778	-0.1092	-0.1936	1.1025	0.2202	0.7495	-13.3994	93.7158	-9.5987
7	4.4912	1.4781	1.1436	6.1441	0.4373	5.2936	-0.2738	1.0134	-0.2379	-0.8166	-0.1627	-0.5534	0.3306	0.907	0.0983	0.3729	0.0301	0.1174	0.5405	0.2036	0.0781	-30.4695	80.3919	-21.0017
8	6.4751	5.0333	-4.8433	6.5335	-2.7798	3.9919	0.0889	1.9351	-0.1649	-2.4814	0.2888	-2.2997	-0.1496	3.9525	-0.2139	0.9235	0.0139	0.4195	1.5223	0.2186	0.82	-21.5987	78.7915	-31.5754
9	4.2753	-1.409	-4.651	6.0152	0.454	7.3229	-0.2407	-0.4461	-0.0497	-0.5156	-0.58	-2.4252	-0.3446	3.0588	0.747	0.3717	-0.1837	0.0941	1.2306	0.3275	0.7299	-13.3061	81.2012	-23.2582
10	4.8793	-1.3623	-1.8269	7.1459	1.1141	0.7369	0.1665	1.4709	-0.3278	-1.3893	-0.2165	-1.4808	1.0703	1.5431	-0.1006	0.9933	0.3947	0.3707	1.5738	-0.0586	0.896	-16.9101	71.6211	-29.7984
11	4.7541	-1.1636	0.0901	8.6234	0.2579	2.8371	-0.1157	0.3388	-1.2276	-0.6876	-0.267	0.5145	0.5255	0.3432	0.3085	0.491	0.0754	0.0824	0.3669	-0.0874	0.4979	-41.173	64.3698	-19.3355
12	7.535	-6.0886	-4.5818	5.9955	5.5913	6.1025	1.2822	1.3579	0.7343	-1.7793	-1.0846	-0.8051	-1.7316	-0.0645	-0.3983	0.9315	0.3937	0.2367	0.6803	-0.1153	0.7181	-30.5329	54.8313	-33.6857
13	3.2259	-3.0383	-0.5719	2.8797	0.3693	1.8193	-0.2026	-0.0527	-0.7652	-0.1868	-0.0589	0.7089	0.1283	-0.1853	-0.0822	0.7976	0.1749	0.3755	0.2203	-0.2017	0.9329	-33.4168	50.4995	-21.3877
14	7.125	-6.1282	-5.6674	5.9768	6.5017	8.2581	0.6408	0.4727	0.0463	-1.0757	-0.7057	-0.1184	-0.4704	-0.3416	0.528	0.4194	0.031	0.0336	0.3793	0.0573	0.4001	-45.9537	75.0078	-3.6525
15	7.5428	-2.6875	-3.5804	1.8654	2.8999	4.6096	-0.1076	0.385	-1.8407	0.5136	-0.7411	0.7284	0.169	-0.267	0.3433	0.5037	0.0601	0.1611	0.3352	0.0435	0.4682	-44.8708	68.2263	-8.318
16	3.3292	-1.1124	-2.32	8.8734	6.0092	7.6038	-0.2978	-0.7399	-1.5206	1.019	-0.9396	1.7527	0.9419	-1.0053	0.8043	0.4331	-0.0156	0.2549	0.5587	0.0989	0.6922	-51.929	66.0595	-0.1615
17	2.9198	-0.3416	-0.2099	1.8447	-2.4015	5.6043	-0.3735	-0.3829	-1.4615	0.0968	0.275	0.4657	0.9905	-0.3188	0.2043	0.3306	0.05	0.4152	0.1784	0.2536	0.646	-44.2121	54.519	5.0304
18	5.0273	0.9198	3.976	5.4865	3.597	4.6926	0.0584	1.1846	-2.9045	-1.0351	0.3736	-0.4307	0.8417	1.1558	0.0839	0.8565	0.1401	0.3647	0.7556	-0.0726	1.5459	-38.6999	51.0774	-1.6313
19	2.156	-1.1372	0.0207	2.0636	-0.9827	2.5093	-0.4776	-1.3328	-1.2953	0.459	0.3539	0.5088	0.6992	0.295	-0.0994	0.894	0.3255	0.3065	0.8515	0.4822	0.9881	-41.6855	53.3219	11.2184
20	3.8777	-2.7644	1.576	3.4018	1.9549	7.7707	0.7312	0.219	-0.1536	-0.2663	-0.7519	0.9124	-0.2419	0.5002	-0.3443	0.3919	0.021	0.0359	0.4938	0.0765	0.3481	-40.8878	84.2855	-1.2739
21	2.5694	-2.8286	2.4386	3.1318	-2.9387	6.9379	-0.5318	-0.5578	-0.6334	-0.0773	0.6567	-0.1079	0.562	0.5047	-0.0382	0.3047	0.1	0.0968	0.4834	0.0604	0.5173	-42.3233	75.7092	2.9784
22	6.5077	3.5102	-3.0328	5.9599	-4.0603	6.4302	0.396	-1.7452	0.9634	1.556	-0.503	0.868	-0.6289	0.364	0.0633	0.545	-0.0229	0.0343	0.7048	-0.201	0.3757	-42.1248	83.5089	10.7728
23	4.2062	-0.7819	1.5163	6.7753	2.1	4.7836	-0.0794	-1.8212	-0.2842	1.9106	-0.0241	-0.7175	0.1559	0.5256	-0.1593	0.6774	0.0632	-0.1821	1.0534	0.1464	0.4146	-31.0845	78.9159	17.3637
24	4.1774	-1.6587	1.1041	6.0189	-1.5081	3.3142	-1.7135	-2.6957	0.1572	0.9477	0.7221	0.0249	-1.064	-0.945	-1.522	0.8955	0.2331	-0.1026	1.5546	0.3499	0.7249	-30.0015	70.3532	24.3751
25	3.1643	1.3754	0.9282	7.8716	3.1166	4.5813	-0.0785	-1.0443	-0.2133	0.4746	0.7739	-1.7435	0.159	1.5211	-0.0732	0.693	0.0679	-0.3882	1.2155	-0.1197	0.7619	-22.6196	78.8623	21.5972
26	2.0002	-0.7992	-2.9391	2.7998	1.5428	2.813	0.3237	-1.1361	3.8324	1.6133	0.3669	0.13	0.7631	1.1996	0.3779	1.0757	-0.0682	-0.1945	1.3666	-0.1761	0.9255	-35.2638	89.4394	18.6863

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq -5:61)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 62:72)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 73:87)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 88:106)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 107:124)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 125:143)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq -2:52)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 53:61)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 62:82)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 83:144)
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq -2:61)
12	X-RAY DIFFRACTION	12	chain 'C' and (resseq 62:72)
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 73:143)
14	X-RAY DIFFRACTION	14	chain 'D' and (resseq -1:7)
15	X-RAY DIFFRACTION	15	chain 'D' and (resseq 8:20)
16	X-RAY DIFFRACTION	16	chain 'D' and (resseq 21:34)
17	X-RAY DIFFRACTION	17	chain 'D' and (resseq 35:76)
18	X-RAY DIFFRACTION	18	chain 'D' and (resseq 77:82)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 83:143)
20	X-RAY DIFFRACTION	20	chain 'E' and (resseq -2:7)
21	X-RAY DIFFRACTION	21	chain 'E' and (resseq 8:20)
22	X-RAY DIFFRACTION	22	chain 'E' and (resseq 21:34)
23	X-RAY DIFFRACTION	23	chain 'E' and (resseq 35:66)
24	X-RAY DIFFRACTION	24	chain 'E' and (resseq 67:87)
25	X-RAY DIFFRACTION	25	chain 'E' and (resseq 88:137)
26	X-RAY DIFFRACTION	26	chain 'E' and (resseq 138:144)

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-Basic information

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-Download

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+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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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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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi