PDB-3da7: A conformationally strained, circular permutant of barnase

ID or keywords:

Entry

Database: PDB / ID: 3da7

Title

A conformationally strained, circular permutant of barnase

Components

Barnase circular permutant
Barstar

Keywords

PROTEIN BINDING / CIRCULAR PERMUTANT / PROTEIN-PROTEIN COMPLEX / ENDONUCLEASE / Cytoplasm

Function / homology

Function and homology information

Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region / cytoplasm
Similarity search - Function

Biological species

Bacillus amyloliquefaciens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.25 Å

Authors

Mitrousis, G. / Butler, J. / Loh, S.N. / Cingolani, G.

Citation

Journal: Biochemistry / Year: 2009
Title: Structural and thermodynamic analysis of a conformationally strained circular permutant of barnase.
Authors: Butler, J.S. / Mitrea, D.M. / Mitrousis, G. / Cingolani, G. / Loh, S.N.

History

Deposition	May 28, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 14, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Aug 30, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3da7.cif.gz	325.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3da7.ent.gz	267.6 KB	Display	PDB format
PDBx/mmJSON format	3da7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3da7_validation.pdf.gz	480.1 KB	Display	wwPDB validaton report
Full document	3da7_full_validation.pdf.gz	498.1 KB	Display
Data in XML	3da7_validation.xml.gz	34.7 KB	Display
Data in CIF	3da7_validation.cif.gz	49.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/da/3da7 ftp://data.pdbj.org/pub/pdb/validation_reports/da/3da7	HTTPS FTP

-
Related structure data

Related structure data	1brsS S: Starting model for refinement
Similar structure data	1x1w-1 1b3s-1 1bgs-3 1x1w-2 2sam-1 3mab-d 1b2s-1 1hwr-d 1b27-1 1x1u-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) 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

Related structure data

1brsS

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Barnase circular permutant

B: Barnase circular permutant

C: Barstar

D: Barstar

E: Barnase circular permutant

F: Barstar

G: Barnase circular permutant

H: Barstar

91.4 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Barnase circular permutant

D: Barstar

defined by author
22.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Barnase circular permutant

C: Barstar

defined by author
22.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Barnase circular permutant

F: Barstar

defined by author
22.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Barnase circular permutant

H: Barstar

defined by author
22.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	38.879, 80.237, 81.922
Angle α, β, γ (deg.)	88.100, 76.980, 79.470
Int Tables number	1
Space group name H-M	P1

#1: Protein	Barnase circular permutant Mass: 12501.869 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00648*PLUS
#2: Protein	Barstar / Ribonuclease inhibitor Mass: 10352.739 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P11540
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.68 Å³/Da / Density % sol: 54.06 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1M Tris, 14% peg 8k, 150mM (NH4)2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CHESS

/ Beamline: A1 / Wavelength: 0.972 Å

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 10, 2006

Radiation

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

Radiation wavelength

Wavelength: 0.972 Å / Relative weight: 1

Reflection

Resolution: 2.15→30 Å / Num. obs: 50783 / % possible obs: 96 % / Redundancy: 3 % / R_merge(I) obs: 0.109 / Χ²: 6.279 / Net I/σ(I): 17

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2.15-2.23	2.2	0.392	5057	5.944	95.2
2.23-2.32	2.6	0.418	5032	8.261	95
2.32-2.42	3	0.421	5100	9.236	96.5
2.42-2.55	3.4	0.386	5126	8.452	97.4
2.55-2.71	3.5	0.296	5150	7.102	97.4
2.71-2.92	3.5	0.194	5163	5.277	97.6
2.92-3.21	3.4	0.119	5171	4.591	97.5
3.21-3.67	3.1	0.074	5121	4.606	97.2
3.67-4.63	2.9	0.055	4965	4.712	94.1
4.63-30	2.9	0.05	4898	4.739	92.5

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
ADSC	Quantum	data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 1brs

1brs

Resolution: 2.25→19.87 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.899 / SU B: 12.107 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.234 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25	2198	5.1 %	RANDOM
R_work	0.205	-	-	-
obs	0.207	42697	94.93 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 37.599 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.03 Å²	0.01 Å²	-0.02 Å²
2-	-	0.15 Å²	0.02 Å²
3-	-	-	-0.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→19.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6173	0	0	372	6545

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	6303
X-RAY DIFFRACTION	r_angle_refined_deg	1.064	1.947	8534
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	15.142	5	763
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.673	24.433	300
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.474	15	1081
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.09	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	926
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4774
X-RAY DIFFRACTION	r_nbd_refined	0.25	0.2	3132
X-RAY DIFFRACTION	r_nbtor_refined	0.325	0.2	4383
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.189	0.2	471
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.328	0.2	80
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.244	0.2	24
X-RAY DIFFRACTION	r_mcbond_it	2.093	1.5	3825
X-RAY DIFFRACTION	r_mcangle_it	2.491	2	6119
X-RAY DIFFRACTION	r_scbond_it	3.162	3	2478
X-RAY DIFFRACTION	r_scangle_it	4.822	4.5	2415

LS refinement shell

Resolution: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.29	146	-
R_work	0.238	2960	-
all	-	3106	-
obs	-	-	93.61 %

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	2.4018	-0.6343	1.3185	0.7578	-0.4135	3.6686	0.1238	0.0164	-0.0118	0.0014	-0.1889	0.0185	0.1967	0.0734	0.0651	0.0323	0.0061	0.0207	0.0257	0.0469	0.054	-0.8612	-6.0128	7.79
2	12.7414	-7.7819	-17.0647	9.8647	0.8527	40.7702	0.508	0.0349	0.3942	-1.2508	0.1963	-0.9185	-1.0365	-1.215	-0.7043	0.2876	-0.1049	-0.0857	-0.0546	0.0234	0.109	-3.0677	-20.3887	15.0934
3	3.7976	-0.0683	-0.9367	2.2892	-2.695	6.4369	0.023	-0.2083	-0.1045	-0.0706	-0.1387	-0.1124	0.2883	0.3432	0.1158	0.0331	0.135	0.0335	0.0802	0.0813	0.051	7.6107	-12.2212	10.8987
4	4.4326	-7.6412	-6.7727	29.0749	14.0726	17.3426	0.5718	0.4034	0.9143	-1.7268	-1.0324	-2.2824	-0.6922	0.27	0.4605	0.0184	0.277	0.2475	0.1565	0.1947	0.0753	14.4043	-5.1021	-4.9004
5	1.7347	-0.6647	-0.1339	2.3066	-0.4115	2.455	0.2387	-0.0037	0.1378	-0.3253	-0.2625	-0.3156	0.1356	0.3198	0.0238	0.1041	0.0819	0.0265	0.0734	0.0596	0.0094	4.5267	-3.5627	0.8602
6	2.1995	1.0795	-1.9002	1.6495	-1.1742	5.2542	0.0576	-0.0045	0.0645	0.0507	0.0388	0.0972	-0.3348	-0.0266	-0.0964	0.041	0.0064	0.022	-0.018	-0.0047	0.0607	-18.9821	39.5801	-46.8457
7	6.5128	3.7767	-2.572	2.259	-0.8929	6.2088	-0.0722	0.4527	0.1081	0.0349	0.0878	0.0469	-0.7592	-0.1312	-0.0156	0.1697	0.0107	-0.0095	-0.0478	0.026	0.0428	-16.0882	47.4942	-53.1831
8	1.7936	1.7489	-0.0397	4.5385	-3.6398	6.7425	0.1937	-0.1697	-0.1568	0.2	-0.416	-0.1931	-0.3914	0.3562	0.2223	0.0838	-0.091	-0.0137	0.0388	0.0416	0.0393	-7.6506	44.0588	-47.8911
9	4.2871	5.0174	2.4945	10.3789	1.1592	7.1225	0.8396	-0.3864	-0.2375	1.4301	-0.945	-0.6698	-0.6316	0.4991	0.1054	0.3514	-0.3703	-0.1589	0.1733	0.1093	-0.0257	-7.8027	41.8082	-32.6114
10	7.8089	0.8029	2.8576	2.0439	-1.9798	7.9462	-0.003	0.5764	0.155	-0.0155	0.0912	-0.039	0.556	-0.3092	-0.0882	0.0607	-0.0617	0.0224	0.065	-0.0008	0.0343	-20.9843	29.9443	-49.1938
11	6.1266	0.6847	0.4773	2.2654	-0.4806	2.4963	-0.0412	-0.2314	0.1907	-0.0059	0.132	0.0052	-0.2071	-0.4923	-0.0907	-0.0067	0.0046	0.0313	0.0316	-0.0189	0.1058	-30.0794	23.6838	-27.8838
12	1.8702	1.7178	-2.6216	1.7949	-1.3583	8.7506	0.0477	-0.0291	0.0545	0.1832	-0.0384	0.1391	-0.3475	-0.246	-0.0093	-0.0138	0.0555	0.0128	0.0569	0.0219	0.0975	-26.3336	33.1913	-31.2148
13	1.4483	-1.3488	0.2067	2.7436	-2.3864	3.3266	0.0256	0.0084	0.046	0.1187	-0.0001	0.0098	-0.3226	0.1651	-0.0255	0.0336	-0.0346	0.021	0.0179	-0.003	0.0751	-17.227	30.3471	-30.9947
14	14.4928	3.2559	8.1733	4.5261	1.0461	8.7679	0.0015	0.0131	-0.4373	-0.0637	0.1293	0.1875	-0.0443	-0.1389	-0.1307	-0.0329	0.0091	0.0322	-0.0111	-0.0088	0.0984	-29.5879	15.2465	-30.9448
15	3.9644	-0.8991	-0.8263	0.7238	0.1832	3.0372	0.0448	0.1132	0.1392	-0.1836	-0.1061	-0.0924	0.0233	0.0022	0.0614	0.0128	-0.0063	0.0141	0.0079	0.0011	0.0807	-17.7283	20.5334	-33.4127
16	23.8969	-7.245	-12.3672	3.1674	2.5321	7.927	-0.1718	1.2003	0.4325	0.1087	0.2614	-0.2303	0.1014	-0.7447	-0.0896	-0.0209	-0.0027	-0.0214	0.0404	-0.0362	0.0804	-8.1838	13.4257	-14.7175
17	2.2242	-0.5851	0.0192	1.6794	-0.3413	1.044	0.1506	0.0255	-0.027	0.0249	-0.0626	0.0712	0.099	-0.1486	-0.088	0.0454	-0.0127	-0.0045	0.0406	0.0237	0.0542	-7.2352	4.3629	-5.7035
18	6.3972	-2.835	-0.7431	3.7418	-0.6328	0.4587	0.0749	0.1009	0.117	-0.0826	-0.0006	0.1894	0.1146	-0.0245	-0.0744	0.0016	0.0063	-0.0216	0.0216	-0.0249	0.0635	-4.7724	14.1215	-9.7786
19	14.9257	0.8104	1.4322	0.1534	-0.3571	1.8655	0.2736	-0.4609	0.214	0.2528	-0.1749	0.0201	-0.0571	-0.0642	-0.0987	0.0815	0.0104	0.0167	0.0186	0.0196	0.0399	-1.2549	14.2223	-1.4587
20	6.0845	-3.771	1.6066	4.9455	-2.5102	3.8913	-0.0173	0.2745	0.0634	0.3796	-0.2726	-0.0844	0.004	0.2491	0.2899	0.0104	0.0199	-0.0228	0.0382	-0.0223	0.0565	4.7782	14.2708	-9.2431
21	1.8838	0.6037	1.5371	1.2792	0.3068	4.3962	0.0771	0.0082	-0.0107	0.1047	-0.0566	-0.0123	0.2695	-0.1035	-0.0205	0.0729	-0.043	0.0174	-0.0109	-0.0257	0.0467	-3.0975	66.5985	-44.2546
22	3.2933	1.769	1.5406	3.1412	0.9351	4.3748	-0.0646	0.2319	0.0914	-0.1893	0.0923	0.0151	0.2788	0.1593	-0.0276	0.0797	-0.0191	-0.0251	-0.0372	-0.0116	0.0277	-1.3319	62.7763	-49.9455
23	1.8118	0.0115	-0.6803	3.8686	9.6261	36.0236	0.1223	-0.3842	-0.1875	0.2217	-0.5551	0.5189	1.2407	-1.8752	0.4328	0.0343	-0.1812	0.0354	0.1893	-0.0005	0.1183	-13.6326	63.8374	-41.3416
24	1.9195	0.7236	-1.8262	7.1392	1.9442	12.5746	0.2631	-0.2773	-0.0179	1.0675	-0.3149	0.5922	1.0889	-0.9063	0.0518	0.2152	-0.3157	0.1104	0.2222	-0.0104	-0.0031	-11.256	62.7778	-28.1065
25	0.4193	0.0974	1.5333	3.4209	1.0428	5.7459	-0.2132	-0.0174	0.4089	-0.2623	0.0196	0.1875	-0.1662	0.0827	0.1936	0.0033	-0.0434	-0.0062	0.0136	0.0117	0.0819	-2.3054	75.2503	-46.0296
26	1.011	0.662	0.0681	2.8346	0.9603	1.9559	0.0568	-0.039	-0.0417	0.1105	0.0245	-0.1383	0.2682	0.1147	-0.0812	0.0119	0.005	-0.0156	0.0176	-0.0085	0.0716	5.3137	78.6823	-29.6498
27	13.2348	8.6331	2.6743	8.1506	4.4374	3.419	0.0154	-0.5879	-0.2521	0.5951	-0.2825	-0.3579	0.5273	0.1765	0.2671	0.0098	-0.0228	0.0404	0.0226	0.006	0.0887	-3.8742	82.5466	-23.3608
28	2.4263	-0.8248	-0.0803	4.9657	3.2025	5.3408	0.2299	0.1658	0.1516	-0.2505	0.0482	-0.2296	-0.3131	0.0891	-0.2781	-0.0206	-0.0101	-0.017	0.0397	-0.0045	0.1164	9.203	92.2641	-32.5617
29	17.1643	0.7749	-2.0979	2.3289	-0.5716	0.3556	0.2246	0.3215	-0.0388	-0.1669	-0.2916	0.1421	-0.34	-0.111	0.0669	0.038	0.0026	0.0104	0.0376	-0.0704	0.0454	-3.4404	85.6442	-35.5921
30	1.3909	1.0692	2.0939	6.9537	-0.49	3.8725	0.0154	-0.0405	0.0512	0.1965	-0.1081	0.0723	-0.0703	-0.1684	0.0927	-0.0663	0.0056	0.0197	0.0533	-0.0445	0.1027	-3.8144	89.0346	-26.5189
31	10.3274	-0.3029	8.984	8.3068	9.9836	20.4693	0.2793	-0.8498	-0.4891	0.8305	-0.2159	0.4955	1.8399	-1.8272	-0.0634	0.0923	-0.1215	0.0279	0.1804	0.0044	0.1405	-3.4322	37.8971	16.1474
32	0.6328	0.1521	0.2787	0.8145	-1.4143	4.3828	-0.0176	0.0124	0.0905	0.1426	-0.0494	-0.0757	-0.6376	-0.1503	0.067	0.1001	0.0263	-0.0022	-0.0049	-0.03	0.075	3.4606	48.8643	5.871
33	21.8158	-0.0193	-1.8463	12.8701	-1.3754	8.8208	-0.5604	-1.222	0.8731	1.1465	0.5923	-0.5189	-2.2622	-1.784	-0.0319	0.3098	0.3457	-0.0832	0.2299	-0.1225	0.0446	-5.9771	55.2885	13.1532
34	2.8639	3.3103	2.9265	8.673	10.8128	24.2819	-0.3869	0.1976	0.0731	-0.0091	0.0028	0.6441	-0.6318	-0.8159	0.3841	-0.0089	0.1712	0.0052	0.0952	-0.0205	0.0755	-8.9045	49.3807	-1.4815
35	2.0961	-0.6744	0.5987	1.2002	-0.5742	3.9224	0.1136	-0.0457	-0.0223	-0.1609	-0.0498	0.2146	-0.1574	-0.3301	-0.0639	0.0403	0.0671	-0.0202	0.0158	-0.0476	0.0478	-2.1245	45.5579	-1.9753
36	13.0964	-12.5739	6.5464	12.1163	-6.5901	5.3798	-0.1369	0.1655	-0.4963	-0.2551	0.3862	0.1854	-0.3688	0.2398	-0.2493	-0.0137	0.0199	0.0288	0.0058	0.0374	0.139	10.5782	27.7418	-15.5209
37	1.6975	-2.172	0.8337	3.6513	0.4222	2.9511	0.1527	0.083	0.1965	-0.2786	-0.0625	-0.3134	-0.1423	0.3929	-0.0902	-0.0014	-0.0243	0.0432	0.0666	-0.0042	0.099	13.9085	36.246	-8.4156
38	1.4593	-0.1533	-0.3824	2.1577	0.4351	0.6943	0.0642	0.0051	0.0756	-0.0691	-0.0793	0.1399	-0.114	0.0305	0.0152	0.0236	0.0291	0.0168	0.0345	0.0096	0.0546	2.861	35.3646	-8.3206
39	12.3515	-2.1872	7.6869	0.5179	-1.4225	9.5205	0.1563	0.2043	-0.3367	0.1017	0.1856	0.0144	0.5159	0.3633	-0.342	-0.03	0.0294	0.028	0.0525	-0.0117	0.1115	14.3025	20.5064	-7.0771
40	3.6578	-0.9177	0.397	1.9521	0.4211	3.4941	-0.0588	-0.1244	0.1637	0.0491	-0.0227	0.0614	0.1017	-0.0505	0.0815	0.0222	0.0117	0.0128	-0.0116	-0.0252	0.0726	2.5075	27.1881	-5.3529

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	4 - 45	3 - 44
2	X-RAY DIFFRACTION	2	A	A	46 - 51	45 - 50
3	X-RAY DIFFRACTION	3	A	A	52 - 73	51 - 72
4	X-RAY DIFFRACTION	4	A	A	74 - 80	73 - 79
5	X-RAY DIFFRACTION	5	A	A	81 - 112	80 - 111
6	X-RAY DIFFRACTION	6	B	B	3 - 42	2 - 41
7	X-RAY DIFFRACTION	7	B	B	43 - 59	42 - 58
8	X-RAY DIFFRACTION	8	B	B	60 - 74	59 - 73
9	X-RAY DIFFRACTION	9	B	B	75 - 100	74 - 99
10	X-RAY DIFFRACTION	10	B	B	101 - 111	100 - 110
11	X-RAY DIFFRACTION	11	C	C	1 - 20	1 - 20
12	X-RAY DIFFRACTION	12	C	C	21 - 35	21 - 35
13	X-RAY DIFFRACTION	13	C	C	36 - 52	36 - 52
14	X-RAY DIFFRACTION	14	C	C	53 - 65	53 - 65
15	X-RAY DIFFRACTION	15	C	C	66 - 90	66 - 90
16	X-RAY DIFFRACTION	16	D	D	2 - 10	2 - 10
17	X-RAY DIFFRACTION	17	D	D	11 - 44	11 - 44
18	X-RAY DIFFRACTION	18	D	D	45 - 64	45 - 64
19	X-RAY DIFFRACTION	19	D	D	65 - 79	65 - 79
20	X-RAY DIFFRACTION	20	D	D	80 - 90	80 - 90
21	X-RAY DIFFRACTION	21	E	E	3 - 37	2 - 36
22	X-RAY DIFFRACTION	22	E	E	38 - 62	37 - 61
23	X-RAY DIFFRACTION	23	E	E	63 - 77	62 - 76
24	X-RAY DIFFRACTION	24	E	E	78 - 96	77 - 95
25	X-RAY DIFFRACTION	25	E	E	97 - 112	96 - 111
26	X-RAY DIFFRACTION	26	F	F	1 - 46	1 - 46
27	X-RAY DIFFRACTION	27	F	F	47 - 53	47 - 53
28	X-RAY DIFFRACTION	28	F	F	54 - 67	54 - 67
29	X-RAY DIFFRACTION	29	F	F	68 - 82	68 - 82
30	X-RAY DIFFRACTION	30	F	F	83 - 90	83 - 90
31	X-RAY DIFFRACTION	31	G	G	2 - 6	1 - 5
32	X-RAY DIFFRACTION	32	G	G	7 - 46	6 - 45
33	X-RAY DIFFRACTION	33	G	G	56 - 65	55 - 64
34	X-RAY DIFFRACTION	34	G	G	66 - 78	65 - 77
35	X-RAY DIFFRACTION	35	G	G	79 - 112	78 - 111
36	X-RAY DIFFRACTION	36	H	H	3 - 10	3 - 10
37	X-RAY DIFFRACTION	37	H	H	11 - 34	11 - 34
38	X-RAY DIFFRACTION	38	H	H	35 - 55	35 - 55
39	X-RAY DIFFRACTION	39	H	H	56 - 64	56 - 64
40	X-RAY DIFFRACTION	40	H	H - P	65 - 91	65 - 1

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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