PDB-4hqb: Crystal structure of DdrB from Deinococcus radiodurans bound to ssDNA

ID or keywords:

Entry

Database: PDB / ID: 4hqb

Title

Crystal structure of DdrB from Deinococcus radiodurans bound to ssDNA

Components

5'-D(*TP*TP*TP*T)-3'
5'-D(P*TP*TP*TP*TP*T)-3'
Single-stranded DNA-binding protein DdrB

Keywords

DNA BINDING PROTEIN/DNA / DNA annealing / DNA BINDING PROTEIN-DNA complex

Function / homology

Single-stranded DNA binding protein DdrB-like / DdrB-like protein / cellular response to desiccation / double-strand break repair via single-strand annealing / cellular response to gamma radiation / single-stranded DNA binding / DNA repair / DNA / Single-stranded DNA-binding protein DdrB

Function and homology information

Biological species

Deinococcus radiodurans (radioresistant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.301 Å

Authors

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

Citation

Journal: Nucleic Acids Res. / Year: 2013
Title: Crystal structure of the DdrB/ssDNA complex from Deinococcus radiodurans reveals a DNA binding surface involving higher-order oligomeric states.
Authors: Sugiman-Marangos, S.N. / Peel, J.K. / Weiss, Y.M. / Ghirlando, R. / Junop, M.S.

History

Deposition	Oct 25, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 4, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 11, 2013	Group: Database references
Revision 1.2	Dec 4, 2013	Group: Database references
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	Sep 20, 2023	Group: Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4hqb.cif.gz	266.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4hqb.ent.gz	214.4 KB	Display	PDB format
PDBx/mmJSON format	4hqb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4hqb_validation.pdf.gz	470.6 KB	Display	wwPDB validaton report
Full document	4hqb_full_validation.pdf.gz	475.8 KB	Display
Data in XML	4hqb_validation.xml.gz	25.9 KB	Display
Data in CIF	4hqb_validation.cif.gz	36.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hq/4hqb ftp://data.pdbj.org/pub/pdb/validation_reports/hq/4hqb	HTTPS FTP

-
Related structure data

Related structure data	4exwS S: Starting model for refinement
Similar structure data	4c3b-2 4okq-1 4ok9-1 4exw-d 4c3e-2 3zjb-d 4mlw-2 6eho-d 1wrn-1 4h4l-2 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

-
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

M: 5'-D(*TP*TP*TP*T)-3'

N: 5'-D(P*TP*TP*TP*TP*T)-3'

87.2 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

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

M: 5'-D(*TP*TP*TP*T)-3'

N: 5'-D(P*TP*TP*TP*TP*T)-3'

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

M: 5'-D(*TP*TP*TP*T)-3'

N: 5'-D(P*TP*TP*TP*TP*T)-3'

defined by author
174 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	110.700, 110.700, 58.776
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: 16920.033 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Gene: ddrB, ddrB (DR0070), DR_0070 / Plasmid: pET151/D-Topo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RY80
#2: DNA chain	5'-D(TPTPTPT)-3' Mass: 1171.814 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain	5'-D(PTPTPTPTPT)-3' Mass: 1476.007 Da / Num. of mol.: 1 / Source method*: obtained synthetically
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.39 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 50 mM MES, pH 5.6, 300 mM potassium chloride, 10 mM magnesium chloride, 5% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2012 / Details: mirrors
Radiation	Monochromator: Rosenbaum-Rock double crystal sagittal focusing Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. all: 35736 / Num. obs: 35736 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / B_iso Wilson estimate: 52.34 Å² / R_merge(I) obs: 0.068 / Net I/σ(I): 17.4
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.726 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1844 / % possible all: 100

-
Processing

Software

Name	Version	Classification
CBASS		data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EXW

4exw

Resolution: 2.301→40.295 Å / SU ML: 0.31 / σ(F): 1.96 / Phase error: 27.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.246	1798	5.03 %	RANDOM
R_work	0.1904	-	-	-
obs	0.1931	35711	99.84 %	-
all	-	35736	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 61.3 Å²

Refinement step

Cycle: LAST / Resolution: 2.301→40.295 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4703	160	0	199	5062

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4982
X-RAY DIFFRACTION	f_angle_d	1.07	6787
X-RAY DIFFRACTION	f_dihedral_angle_d	16.112	1728
X-RAY DIFFRACTION	f_chiral_restr	0.07	736
X-RAY DIFFRACTION	f_plane_restr	0.005	857

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 (%)
2.301-2.3632	0.3437	140	0.2551	2656	X-RAY DIFFRACTION	100
2.3632-2.4328	0.2868	137	0.2427	2560	X-RAY DIFFRACTION	100
2.4328-2.5113	0.3024	129	0.2408	2653	X-RAY DIFFRACTION	100
2.5113-2.601	0.3137	141	0.2317	2586	X-RAY DIFFRACTION	100
2.601-2.7051	0.3124	146	0.2375	2608	X-RAY DIFFRACTION	100
2.7051-2.8282	0.2549	155	0.2283	2631	X-RAY DIFFRACTION	100
2.8282-2.9773	0.2956	137	0.2157	2602	X-RAY DIFFRACTION	100
2.9773-3.1637	0.2886	151	0.2142	2582	X-RAY DIFFRACTION	100
3.1637-3.4079	0.2489	152	0.1994	2598	X-RAY DIFFRACTION	100
3.4079-3.7506	0.2624	125	0.1781	2629	X-RAY DIFFRACTION	100
3.7506-4.2928	0.2107	138	0.1658	2588	X-RAY DIFFRACTION	100
4.2928-5.4064	0.2061	124	0.1527	2640	X-RAY DIFFRACTION	100
5.4064-40.3013	0.2203	123	0.191	2580	X-RAY DIFFRACTION	98

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	8.342	-1.4025	3.5494	7.342	-2.3864	8.0732	0.0957	-0.162	0.0841	0.8238	-0.2151	0.0861	-0.3608	0.48	0.1073	0.5474	0.0022	0.1351	0.2786	-0.0856	0.3025	11.0197	29.4155	25.0324
2	5.3839	-2.0519	0.1942	5.8131	-1.2896	0.92	0.0834	0.0678	-0.1239	0.078	-0.1285	0.3021	0.1066	-0.1586	0.0494	0.3571	-0.0523	0.0325	0.2881	-0.0284	0.2544	8.0475	15.1763	22.1788
3	9.3525	-3.2718	0.6523	7.5604	2.2054	4.1428	0.1014	0.1521	-0.421	-0.0511	-0.4323	0.562	-0.062	-0.5827	0.3092	0.2743	-0.0501	0.0509	0.2899	0.0507	0.1797	1.5019	7.1958	17.4315
4	1.903	-0.0688	2.2885	1.8164	-2.1647	6.8119	0.0218	0.1756	0.0327	-0.006	0.0008	-0.0653	-0.1421	0.1283	-0.0325	0.2663	0.0341	0.0259	0.2653	-0.0204	0.4052	6.6733	10.4073	14.143
5	4.8582	6.8626	3.9595	2.0848	4.9738	6.7978	-0.1959	-0.4694	0.4316	0.1641	0.059	-0.215	-0.5065	0.1737	0.2153	0.4188	-0.0229	-0.0058	0.3645	0.0092	0.5684	23.0576	28.3503	20.1841
6	7.3197	-1.3607	-0.3959	5.0608	0.8962	5.8623	0.0144	-0.0232	-0.2696	-0.1568	-0.2229	-1.1271	-0.0079	0.7592	0.1383	0.2985	-0.0189	0.0738	0.3819	0.0983	0.579	32.1182	19.0149	14.6823
7	3.6947	2.8177	-0.1481	4.7068	-4.5245	7.4017	0.3438	0.5313	-0.3433	-0.195	-0.2917	-0.5567	0.2997	0.2326	0.0191	0.3643	0.0944	-0.0092	0.3698	-0.0727	0.4599	26.6748	4.8706	14.8116
8	3.6825	-4.1971	-2.1755	9.861	-0.6277	3.1737	0.3764	0.0974	-0.7781	-0.9553	-0.3662	-0.643	0.2804	0.6996	0.0149	0.4246	0.0562	0.025	0.6379	-0.0182	0.5647	29.1642	5.4712	5.8414
9	3.5749	1.8363	1.6737	5.3867	-3.1893	4.6518	-0.6119	0.634	-0.4278	-0.6688	0.0179	-0.2851	-0.1599	0.7505	0.5932	0.5531	0.0364	0.1324	0.5958	-0.0662	0.4312	32.4831	7.9386	1.2843
10	2.7261	2.3441	-1.0618	3.5147	-4.0004	6.9544	0.246	0.9961	0.9218	-1.4391	0.2414	1.134	-0.2118	0.0969	-0.6324	0.7145	-0.0109	0.028	0.7029	0.0751	0.643	18.1967	11.9396	-1.9762
11	4.378	1.4398	-0.1366	4.7833	0.2658	6.0333	-0.3929	0.7279	-0.217	-0.5956	0.131	-1.3039	-0.7353	1.097	0.2384	0.4075	-0.0511	0.1699	0.5304	0.0275	0.7291	37.512	15.6327	8.1537
12	7.4008	-2.0663	1.2874	3.5494	4.5464	8.2681	0.2667	-0.5488	0.8028	0.2128	-0.0891	-0.353	-0.0847	0.3262	-0.1809	0.3506	-0.0649	0.0583	0.4401	0.0536	0.6104	28.4605	34.6283	11.0034
13	5.354	0.6987	0.9367	3.5994	-1.7259	5.6418	-0.1444	0.5539	1.2797	-0.0966	-0.3307	-0.7109	-0.8986	0.8435	0.4503	0.4995	-0.0954	-0.0068	0.5386	0.1583	0.9974	32.8861	41.35	10.2334
14	8.2097	-0.1558	1.5601	6.5509	-3.3197	2.0419	0.6712	0.1162	0.2468	-0.8087	-0.3607	-0.1619	0.3126	-0.1263	-0.2108	0.4758	0.0672	0.1599	0.4334	0.0927	0.5127	27.6137	33.9832	0.0783
15	0.0057	0.137	-0.1398	0.9251	-1.0319	1.0734	0.4911	0.4111	1.0236	-1.0143	0.4112	-0.9	-0.7238	0.4484	-0.0913	1.1592	0.0152	0.8004	0.6087	0.6877	1.1289	33.0557	43.4308	-8.9195
16	3.6623	-0.4489	-2.2637	1.7905	0.4206	4.2585	0.2007	1.2838	0.675	-0.5658	0.1216	-0.4955	-0.7212	0.9372	-0.2505	0.1775	-0.149	0.6987	0.8417	0.4708	0.9847	39.2581	37.4983	-3.6212
17	1.9125	0.0946	0.1551	0.4125	0.259	8.5559	0.0486	0.3002	-0.2431	-0.6792	0.0706	-0.5891	0.9795	0.9503	0.0541	0.7615	0.1447	0.4277	0.7647	0.2603	0.8823	35.3482	28.8239	-6.0111
18	3.4659	2.3642	-3.2804	1.8276	-1.9749	3.6102	-0.0281	0.4918	0.3392	-0.5176	0.2302	0.371	0.4863	0.0315	-0.0787	0.9276	0.1279	0.3532	0.7944	0.2348	0.8134	34.333	33.0018	-14.9478
19	2.7162	-2.5652	2.257	9.2808	0.0851	2.5806	0.6676	-0.2141	0.0125	1.1276	-0.5933	2.5442	2.3983	-2.0218	-0.1405	1.098	-0.158	0.1578	0.9374	-0.008	1.1722	23.8543	23.1491	-10.1941
20	5.1434	2.7133	1.7434	5.6836	4.2979	7.344	0.2963	0.5341	1.4865	-0.8124	-0.7634	0.3086	-0.7504	0.6075	0.5035	0.9346	-0.0322	0.3576	0.6223	0.3277	0.9952	34.5788	43.3789	-7.5408
21	6.0712	-5.5268	-4.9064	6.5471	6.9843	9.2469	-0.3526	0.1023	-0.056	0.6676	-0.4368	-0.038	0.762	0.2195	0.7545	0.5732	-0.1114	0.1654	0.4145	0.045	0.7443	20.4012	44.5089	7.743
22	6.5699	-5.0632	-3.215	4.8919	3.6327	2.9181	-0.4138	-0.3611	-0.5316	2.4282	-1.2336	1.873	0.7922	-1.1279	1.475	0.8043	-0.2287	0.2545	0.6859	-0.1291	0.7283	20.0604	46.4776	13.1424
23	5.0161	-0.9053	-3.024	2.2816	-2.0146	8.308	0.4959	-0.0207	1.0197	0.7229	0.183	0.5363	-1.5276	-0.2096	-0.7021	0.7833	-0.0672	0.1567	0.4424	0.0459	0.9934	16.4859	54.6603	7.5304
24	4.5992	5.4755	3.7384	8.6129	1.0169	8.1132	-0.2068	-0.5399	-1.0248	-0.3131	-0.1984	0.5437	0.2746	-0.6344	0.2911	0.3642	0.0416	0.0954	0.3622	-0.056	0.7891	12.9985	43.2848	-0.3612
25	2.8874	-2.7828	-0.9473	2.8608	2.0422	6.4348	0.1767	1.3565	0.6167	-0.3807	-0.432	1.4626	-0.9794	-1.3958	0.2268	0.4982	0.1201	0.1149	0.7436	0.1625	1.3941	2.6292	52.5403	-3.2025
26	6.1729	1.5526	-1.4591	3.1023	2.3738	3.1362	0.0739	0.494	0.5868	-0.3395	-0.3121	0.9868	-1.1487	-0.5764	0.2501	0.5696	0.0623	0.0314	0.4933	0.0247	1.0907	9.9037	55.9476	-3.5316
27	6.8489	-4.0239	5.6016	8.6103	-2.7983	6.1999	-0.1592	1.5378	0.9253	-0.8953	0.1153	0.0023	-0.0545	0.556	-0.0094	0.5981	-0.144	0.0239	0.598	0.1858	0.9429	16.1108	54.7453	-13.2536
28	6.7566	-3.3746	-1.7336	4.1127	1.8256	9.9023	-0.1328	0.66	-0.0644	-0.3743	-0.443	0.0722	0.1461	-0.7673	0.5815	0.6558	-0.0638	-0.156	0.4776	0.0763	0.894	11.7821	47.9117	-11.6945
29	2.0593	0.7007	-2.6975	1.0502	-3.0573	9.2841	-0.5942	0.117	-0.3899	-1.2104	-0.196	1.9049	0.9886	-1.2738	0.8019	0.4747	-0.1778	-0.0642	0.6324	0.0198	1.421	7.756	44.873	-10.5682
30	5.994	1.8641	-1.274	0.5955	-0.9665	8.6384	0.744	-0.6396	1.0752	0.9324	-0.77	2.121	-0.9268	-1.0643	0.1166	0.5979	0.1042	0.432	0.6946	0.2108	1.7778	3.1381	57.8265	1.3252
31	5.4276	-4.8079	5.5503	5.2346	-4.8835	5.5658	-0.5719	-0.6025	0.454	0.5098	0.2876	0.522	-0.9229	1.1115	0.2299	0.5721	-0.0767	0.0632	0.5182	-0.105	0.6058	9.8833	40.125	18.8876
32	6.1489	-0.6773	0.9155	2.6756	2.6118	3.0495	0.2502	-0.17	0.3078	0.1295	-0.0794	0.0705	0.3834	0.0357	-0.1121	0.5443	-0.0474	0.1302	0.2758	0.0592	0.7214	9.3622	44.1254	15.2594
33	7.1621	-0.6494	1.4345	2.0692	1.7644	2.1715	-0.3264	-0.5759	0.7559	1.0877	0.1476	0.1006	-0.6972	-0.6019	0.217	0.7383	0.026	0.2524	0.3962	-0.0512	0.7671	0.8818	44.1399	20.9723
34	7.2697	5.7583	3.9469	4.5321	3.2433	2.3747	0.0097	0.1463	-0.6349	-0.2574	0.477	-1.7789	-0.0943	-0.2286	-0.5232	0.3958	0.036	0.1337	0.3242	0.03	0.6641	1.1936	35.9841	9.1979
35	9.5857	6.819	1.6334	8.7059	0.2077	6.5106	0.3314	-0.3968	0.5745	0.464	-0.161	0.3563	-0.3621	-0.6708	-0.1855	0.3814	0.0803	0.1394	0.3289	-0.0042	0.4523	-10.5224	36.2572	15.376
36	4.2596	-5.172	6.0467	6.8845	-6.3206	9.7603	-0.482	0.0922	1.419	0.2977	0.3893	1.6532	-1.066	-1.1047	0.0644	0.5415	0.1447	0.1191	0.5336	0.1267	1.3143	-16.245	47.0404	6.7897
37	9.1983	5.9005	-1.2192	4.3733	-0.8732	1.9598	-0.0025	0.5619	1.6396	0.0103	0.2763	0.9205	-0.367	-0.2134	-0.2928	0.3993	0.0776	0.0888	0.3267	0.1127	0.677	-10.5362	39.3275	4.2317
38	5.6588	-5.4307	-6.7176	5.532	7.0711	9.1234	0.0911	0.3493	0.1845	-0.0368	-0.573	0.8381	-0.0467	-0.4607	0.4022	0.3354	-0.0303	0.0284	0.3995	-0.008	0.5304	-19.535	17.1537	6.7766
39	5.63	1.8438	-1.07	6.7617	0.5491	2.3057	-0.3717	0.4104	-0.2052	-0.012	0.1274	-0.2049	1.1219	-0.0829	0.314	0.3515	0.0461	0.1426	0.3192	-0.0034	0.4924	-11.4817	31.8658	8.5255
40	8.6928	-0.7569	5.0155	2.0375	-1.2803	9.5708	-0.9134	-0.6777	-0.1383	1.4999	0.4633	-0.209	0.813	-0.6012	0.3983	0.8294	0.1502	0.0848	0.5268	-0.0281	0.5182	-9.9661	39.1174	23.158

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 34 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 35 through 63 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 99 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 100 through 143 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 20 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 21 through 62 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 63 through 79 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 80 through 87 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 88 through 106 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 107 through 124 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 125 through 143 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 12 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 13 through 34 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 35 through 45 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 46 through 52 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 53 through 74 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 75 through 85 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 86 through 106 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 107 through 124 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 125 through 143 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 1 through 12 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 13 through 20 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 21 through 34 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 35 through 45 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 46 through 52 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 53 through 61 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 62 through 77 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 78 through 104 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 105 through 131 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 132 through 143 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 0 through 7 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 8 through 20 )
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 21 through 34 )
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 35 through 45 )
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 46 through 62 )
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 63 through 72 )
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 73 through 87 )
38	X-RAY DIFFRACTION	38	chain 'E' and (resid 88 through 99 )
39	X-RAY DIFFRACTION	39	chain 'E' and (resid 100 through 137 )
40	X-RAY DIFFRACTION	40	chain 'E' and (resid 138 through 144 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
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

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
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