PDB-3iq1: Crystal structure of DPS protein from Vibrio cholerae O1, a membe...

ID or keywords:

Entry

Database: PDB / ID: 3iq1

Title

Crystal structure of DPS protein from Vibrio cholerae O1, a member of a broad superfamily of ferritin-like diiron-carboxylate proteins

Components

DPS family protein

Keywords

METAL TRANSPORT / CSGID / DPS family protein / SAD / NIAID / Structural Genomics / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis
Similarity search - Function

Biological species

Vibrio cholerae O1 biovar El Tor (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.67 Å

Authors

Nocek, B. / Peterson, S. / Gu, M. / Otwinowski, Z. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of DPS protein from Vibrio cholerae O1, a member of a broad superfamily of ferritin-like diiron-carboxylate proteins
Authors: Nocek, B. / Peterson, S. / Gu, M. / Otwinowski, Z. / Anderson, W. / Joachimiak, A.

History

Deposition	Aug 18, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 8, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3iq1.cif.gz	157.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3iq1.ent.gz	136.7 KB	Display	PDB format
PDBx/mmJSON format	3iq1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3iq1_validation.pdf.gz	443.7 KB	Display	wwPDB validaton report
Full document	3iq1_full_validation.pdf.gz	448.3 KB	Display
Data in XML	3iq1_validation.xml.gz	33 KB	Display
Data in CIF	3iq1_validation.cif.gz	49.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iq/3iq1 ftp://data.pdbj.org/pub/pdb/validation_reports/iq/3iq1	HTTPS FTP

-
Related structure data

Related structure data	1jig
Similar structure data	1n1q-2 2clb-2 2qqy-1 4cya-1 2pyb-1 1uvh-1 2chp-1 2clb-1 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
Other databases	TargetDB: IDP01318

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#35 - Nov 2002 Ferritin and Transferrin similarity (3) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: DPS family protein

B: DPS family protein

C: DPS family protein

D: DPS family protein

hetero molecules

73.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DPS family protein

B: DPS family protein

C: DPS family protein

D: DPS family protein

hetero molecules

A: DPS family protein

B: DPS family protein

C: DPS family protein

D: DPS family protein

hetero molecules

A: DPS family protein

B: DPS family protein

C: DPS family protein

D: DPS family protein

hetero molecules

defined by author&software
222 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	93.816, 93.816, 225.561
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

Components on special symmetry positions

ID	Model	Components
1	1	A-461- HOH

#1: Protein	DPS family protein Mass: 18445.859 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria) Strain: N16961 / Gene: VC_0139 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q9KVK4
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 777 / 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: 2.59 Å³/Da / Density % sol: 52.49 %
Crystal grow	Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.4 M Sodium malonate, 0.1 Bis-Tris propane pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 279K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2009 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.67→35 Å / Num. all: 86105 / Num. obs: 85102 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / B_iso Wilson estimate: 28 Å² / R_merge(I) obs: 0.078 / Net I/σ(I): 17
Reflection shell	Resolution: 1.67→1.7 Å / Redundancy: 2 % / R_merge(I) obs: 0.25 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3815 / % possible all: 90.2

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
Coot		model building
MLPHARE		phasing
SHELX		model building
ARP/wARP		model building
REFMAC	5.5.0054	refinement
HKL-3000		data reduction
SCALEPACK		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.67→35 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.961 / SU B: 3.133 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.077 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17381	4268	5 %	RANDOM
R_work	0.13936	-	-	-
all	0.143	85080	-	-
obs	0.14104	80802	98.82 %	-

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: 7.715 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.21 Å²	0.11 Å²	0 Å²
2-	-	0.21 Å²	0 Å²
3-	-	-	-0.32 Å²

Refinement step

Cycle: LAST / Resolution: 1.67→35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5073	0	4	777	5854

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	5331
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3546
X-RAY DIFFRACTION	r_angle_refined_deg	1.502	1.949	7234
X-RAY DIFFRACTION	r_angle_other_deg	0.967	3	8705
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.492	5	679
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.203	25.362	276
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.525	15	988
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.567	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	796
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	6024
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1064
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.858	1.5	3209
X-RAY DIFFRACTION	r_mcbond_other	0.309	1.5	1324
X-RAY DIFFRACTION	r_mcangle_it	1.507	2	5147
X-RAY DIFFRACTION	r_scbond_it	2.755	3	2122
X-RAY DIFFRACTION	r_scangle_it	4.341	4.5	2063
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.67→1.71 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.25	285	-
R_work	0.204	5642	-
obs	-	-	93.07 %

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	4.2898	-0.2625	-0.2402	0.202	1.0235	5.8658	0.1059	0.0182	0.2036	-0.0413	0.0383	-0.0224	-0.1131	0.3476	-0.1442	0.0515	-0.0076	0.0139	0.0888	-0.0104	0.1009	87.4929	39.8579	252.0368
2	1.1623	1.9072	-1.9238	3.5756	-2.2979	4.8543	0.0451	-0.0615	-0.0938	0.1085	0.006	-0.2481	0.0007	0.2874	-0.0511	0.0208	-0.0085	-0.0081	0.1085	-0.0274	0.0985	86.5116	37.2067	262.6585
3	3.385	1.4082	-1.7721	2.1981	-0.7948	1.9775	-0.0477	0.1014	-0.1482	0.1187	-0.0274	-0.1157	0.0137	0.0183	0.0751	0.0575	0.0014	-0.013	0.0674	-0.0065	0.0716	74.4533	26.9922	269.838
4	3.0854	0.6867	-0.044	0.3674	0.3271	0.5371	-0.0217	-0.0848	-0.0632	0.0407	-0.0156	0.0069	0.0569	0.029	0.0372	0.0864	-0.0018	0.0115	0.062	0.0124	0.0839	61.7128	19.153	276.217
5	6.4822	3.5932	-3.3903	4.4328	-2.9578	2.7534	0.1319	0.0284	0.0335	0.1705	-0.0442	0.1547	-0.1467	-0.0869	-0.0877	0.0598	-0.0144	-0.0053	0.0777	-0.0014	0.0568	53.4592	22.9706	275.6655
6	6.9541	3.1535	-0.6928	2.0957	-1.4786	3.3581	-0.2207	0.2822	-0.1041	-0.0476	0.17	-0.0073	-0.0962	-0.0479	0.0507	0.076	-0.0275	-0.0145	0.0886	-0.0057	0.0502	64.0516	27.5272	265.8758
7	6.297	2.3253	-4.4915	4.6741	-5.6566	9.8701	-0.0725	0.1851	-0.0629	-0.1074	0.0665	0.0824	0.0019	-0.51	0.006	0.0936	-0.0263	-0.0076	0.0877	-0.0105	0.0585	73.4685	29.4591	259.6178
8	1.4582	0.3639	0.8524	4.8368	-1.7343	1.4972	-0.009	0.0056	0.0309	-0.0223	0.0121	-0.2733	0.0836	0.1013	-0.0032	0.0989	0.0212	-0.0284	0.1074	-0.0443	0.1236	82.3965	30.3495	258.0289
9	1.9164	0.888	0.5962	0.6896	1.1894	3.3482	-0.0278	-0.0381	-0.0433	0.03	0.0025	-0.0499	0.0768	0.0055	0.0252	0.0673	0.0111	-0.0381	0.0749	-0.016	0.1215	80.3727	19.9743	268.2382
10	5.3431	1.5922	-2.2559	2.0311	-0.5696	1.6846	-0.015	-0.2862	-0.0139	0.2262	-0.003	-0.063	-0.0216	0.1487	0.0179	0.0879	0.0019	-0.0484	0.0727	0.0007	0.0325	72.1839	22.6968	279.8954
11	3.3995	1.7347	-1.0526	1.1084	-0.6667	2.4793	0.1046	-0.047	0.0335	0.1764	-0.0558	0.0307	-0.1746	-0.029	-0.0487	0.1155	0.0027	-0.0052	0.073	0.0082	0.0458	65.6586	31.1434	280.1463
12	3.7545	0.5205	-0.0314	1.4114	1.6093	1.9993	0.1145	-0.0491	-0.0473	0.1927	0.0371	-0.1811	0.1483	0.0164	-0.1516	0.1239	0.0093	-0.0619	0.099	-0.0049	0.0973	75.1327	39.224	272.4936
13	7.662	3.2719	-7.8379	8.5627	-1.2113	8.6571	0.351	-0.2079	0.2387	0.1876	0.0177	-0.2084	-0.3798	0.2573	-0.3687	0.0788	-0.0383	-0.0008	0.0824	-0.0189	0.0997	81.0397	45.2462	265.8512
14	1.046	-0.232	-1.4783	0.214	0.1024	2.4208	0.0096	0.0324	0.0046	0.0236	0.0095	-0.0163	-0.065	-0.0532	-0.0191	0.0709	-0.0079	-0.0043	0.0785	-0.0086	0.0733	70.7406	41.0947	264.2702
15	4.0062	2.4384	-2.563	5.9028	-2.1184	4.1547	0.0296	-0.2016	0.0997	0.1333	0.0498	0.1081	-0.174	-0.0016	-0.0794	0.0771	0.0133	-0.0061	0.0686	-0.0038	0.029	57.6688	36.4631	279.8003
16	2.2738	-2.8045	1.2117	3.5028	-1.4623	0.6719	-0.1224	-0.0477	0.1526	0.1401	0.0446	-0.1982	-0.0983	-0.0342	0.0778	0.1422	0.01	0.0183	0.0924	0.0259	0.0847	39.4408	53.0088	210.1681
17	3.7628	1.9629	1.8941	3.4039	-0.6714	2.7402	-0.0926	0.2054	0.1289	-0.1396	0.1167	0.0583	0.0214	0.0205	-0.0241	0.0931	0.0096	0.0012	0.0754	0.0263	0.0523	38.9309	44.4403	208.7753
18	5.7485	1.4188	-1.5107	2.3274	-1.8605	1.9392	0.0444	0.2975	-0.0129	-0.0658	0.0352	0.0565	-0.1218	-0.1681	-0.0797	0.0933	0.0171	0.0032	0.0981	0.0132	0.0581	30.4397	38.0962	211.5428
19	1.6346	0.798	-1.2879	1.5876	-1.9035	2.4814	-0.0084	0.0346	0.021	0.1618	0.0436	0.085	-0.1327	-0.0345	-0.0352	0.0729	0.0054	0.0113	0.0626	-0.007	0.0585	22.8691	28.6248	226.3177
20	2.2411	1.1562	-0.6486	2.1498	-1.704	2.6784	-0.0507	-0.0019	-0.1827	-0.0192	0.0742	0.1091	0.152	-0.0482	-0.0235	0.0845	-0.0107	0.0172	0.0746	-0.0052	0.0537	18.7034	15.8735	237.8386
21	2.2084	1.7038	-2.0856	3.8078	-2.3633	3.2795	-0.0242	0.028	-0.1361	0.2022	0.1028	-0.0959	-0.119	0.0695	-0.0786	0.0697	-0.0071	-0.0043	0.0838	-0.0006	0.0625	27.3105	22.3668	233.3969
22	3.1413	1.0329	1.6772	10.7761	-2.4989	2.5053	0.0201	-0.2963	0.0696	0.2849	-0.0123	-0.0466	-0.0576	0.0503	-0.0078	0.1054	-0.011	-0.008	0.2027	-0.0175	0.0617	33.1147	33.0088	227.1632
23	5.4239	0.1176	-0.9517	0.8671	0.1676	1.5171	0.071	-0.157	0.2889	-0.0706	-0.1306	0.073	-0.0739	-0.0599	0.0596	0.0682	-0.0167	0.0012	0.0912	-0.029	0.0752	33.4773	42.1803	219.3233
24	1.879	0.9094	0.4522	3.3621	3.0861	4.0255	-0.025	0.1828	0.071	-0.1275	-0.0048	0.1021	-0.1821	-0.216	0.0298	0.0601	0.0247	-0.0155	0.0836	0.0112	0.0463	19.1147	39.0368	220.9696
25	1.6614	0.2661	-0.6485	2.9562	-2.5657	2.3945	-0.0322	0.1249	-0.0747	-0.1651	0.0684	0.1633	0.1714	-0.1043	-0.0362	0.0666	-0.0277	0.0018	0.1024	-0.0295	0.1103	14.9058	22.9954	224.7854
26	2.1523	1.1685	-0.6161	1.4508	-1.2941	2.8474	-0.0502	0.1205	-0.1831	-0.0546	0.0206	-0.0593	0.1192	-0.1192	0.0297	0.0472	-0.0143	0.0012	0.0795	-0.0149	0.0768	22.8745	18.5466	221.902
27	1.5034	2.1504	0.0208	5.0399	-0.9757	3.4848	-0.0355	0.1511	-0.0681	-0.2035	0.0716	-0.0565	-0.0141	-0.2598	-0.0361	0.0554	0.0128	-0.0021	0.0984	-0.0011	0.0389	33.8634	28.0798	210.475
28	2.8096	1.2382	0.0014	5.5532	6.0145	9.4914	-0.0787	0.212	-0.097	-0.4454	0.1777	-0.0436	-0.3482	-0.0703	-0.099	0.0893	-0.0259	0.0157	0.0908	0.0106	0.0425	42.5806	35.1913	208.8769
29	0.7969	1.0489	-0.3998	3.3959	-0.6008	0.4986	0.022	0.0255	-0.0589	0.0798	-0.0337	-0.0712	-0.0145	0.0062	0.0117	0.0583	-0.0075	-0.0039	0.0786	-0.0004	0.0631	37.3669	24.617	219.4686
30	7.0414	1.5035	-3.5833	4.5249	-0.6642	4.1501	-0.104	0.0909	-0.3296	-0.1782	0.134	-0.0687	0.1851	0.0383	-0.03	0.0398	-0.0132	-0.005	0.0656	-0.0053	0.0661	28.1219	10.2051	224.8557
31	3.9797	-0.9595	0.3779	3.482	-2.1254	2.3402	0.055	-0.118	-0.1417	-0.0431	0.11	0.4283	0.2253	-0.192	-0.165	0.0508	-0.0358	0.0112	0.0954	0.0013	0.149	2.6725	22.3594	250.6344
32	0.9854	-0.0464	-0.1011	2.009	-1.8461	2.8452	-0.056	0.0978	-0.0975	-0.1305	0.0874	0.1671	0.0871	-0.267	-0.0314	0.0265	-0.0047	0.0155	0.0972	-0.0195	0.115	4.2695	33.0743	244.8841
33	3.3695	2.1568	-0.973	1.4354	-0.4229	2.1131	-0.0543	0.0973	-0.1342	-0.0853	0.046	-0.0618	-0.065	-0.0182	0.0083	0.075	0.013	-0.0029	0.0728	-0.0063	0.0764	19.3636	41.051	234.5092
34	5.7609	3.6307	0.6847	3.1317	-0.2006	0.715	-0.0626	0.0233	0.0596	-0.1857	0.0361	-0.0666	0.057	-0.1739	0.0265	0.1066	0.0094	0.0358	0.1786	0.012	0.0813	32.523	47.9961	227.4113
35	9.4422	0.7851	-0.1839	3.5596	-4.9573	6.9934	0.275	-0.2455	0.3089	0.3065	-0.1688	0.0954	-0.4018	0.2142	-0.1062	0.0794	0.013	0.0352	0.0805	-0.0064	0.0741	39.096	52.5017	232.6481
36	2.6249	3.3038	-1.7429	4.5512	-1.2841	3.5625	0.0357	0.0451	-0.1575	0.1125	0.0553	-0.243	-0.0841	0.0669	-0.0909	0.0952	-0.006	0.0128	0.0888	0.0068	0.1024	32.4341	44.6989	236.4542
37	10.6331	3.7212	-5.674	4.5273	-1.6546	3.0636	-0.2533	-0.1362	-0.5338	-0.1488	-0.0238	-0.1096	0.1187	0.0682	0.277	0.0707	0.0374	0.0271	0.0899	0.0382	0.1279	25.4856	36.8582	240.5949
38	9.8431	5.3077	-5.8493	3.2644	-4.3663	7.1515	0.0373	-0.0312	-0.1715	-0.0022	-0.064	-0.0934	0.0398	0.1114	0.0267	0.0953	0.0444	0.0684	0.06	0.0342	0.1921	19.3536	30.8081	241.6845
39	1.3729	0.1744	0.0677	1.0213	-1.4464	5.7224	0.0128	-0.0313	-0.0232	-0.184	-0.0832	0.0899	0.2708	-0.1083	0.0704	0.1004	0.021	0.014	0.0664	-0.0056	0.0824	10.7218	27.3444	241.4752
40	1.3593	-2.2225	-0.9285	5.5756	2.168	1.8931	0.0461	0.082	-0.0179	-0.0914	-0.0544	0.2406	-0.049	-0.2293	0.0083	0.0358	0.0271	-0.0148	0.1144	0.004	0.0798	11.9144	35.7728	229.3838
41	2.7918	1.1608	-0.9806	1.3313	0.1389	1.4612	-0.0084	0.0444	0.1215	-0.1	0.0437	0.1379	-0.1801	-0.0904	-0.0353	0.0969	0.0401	-0.0087	0.0527	0.0274	0.0659	20.6859	50.2166	228.9107
42	2.6694	1.9523	-1.5486	2.1657	-1.5883	2.1367	0.0107	0.0081	0.0846	0.036	-0.0218	0.0918	-0.2191	-0.0843	0.0112	0.0731	0.0206	0.0009	0.0688	0.0098	0.0778	19.4479	50.2992	239.9791
43	3.3555	1.6569	-1.525	8.6118	-2.4073	1.9072	0.0568	-0.1634	0.1009	0.1554	-0.127	0.4974	-0.0282	-0.058	0.0701	0.0286	-0.0006	0.039	0.1151	-0.0301	0.1037	7.1286	40.0358	252.2705
44	1.0386	1.6336	-0.3793	2.8195	-0.2441	0.7026	0.0218	0.0007	-0.0458	0.0632	-0.0442	-0.0398	-0.0423	-0.0658	0.0224	0.0626	0.0098	0.0176	0.0743	0.0053	0.0898	17.1785	38.4003	251.7544
45	3.6301	3.8992	-2.2453	5.6098	-3.3773	6.2619	-0.0128	0.0387	0.1445	0.1373	0.0738	0.1572	-0.1406	-0.0293	-0.061	0.0609	0.0226	0.0057	0.0466	0.0066	0.0564	27.7721	54.5776	245.1925
46	0.0252	0.0796	-0.1178	0.2775	-0.4224	0.6494	0.003	0.0004	0.0207	0.0363	0.0151	0.0203	-0.0637	-0.0486	-0.0182	0.1435	0.0067	-0.0038	0.1102	0.0057	0.114	54.4934	1.1778	286.7443
47	8.1305	-1.3726	0.0722	2.182	-2.1427	2.7226	0.0406	-0.2523	-0.2377	-0.0227	-0.1184	-0.0191	0.081	0.1237	0.0779	0.0974	-0.0054	-0.0081	0.076	0.0126	0.0304	57.8378	-2.2741	279.4356
48	1.5911	1.5533	-1.5516	1.9227	-1.3699	2.3433	0.0342	-0.0706	-0.0627	0.1337	-0.0342	-0.1024	-0.1008	0.0146	0	0.07	0.0036	-0.0084	0.0658	0.0086	0.0661	70.2978	6.9452	268.1891
49	1.1947	-1.0268	0.3881	2.5601	-0.7356	0.9386	0.0037	-0.1272	0.0834	0.1158	-0.035	-0.0815	-0.0356	0.1028	0.0313	0.0931	-0.0288	0.0007	0.0688	-0.015	0.0758	78.0543	20.733	254.5718
50	9.9589	-0.7476	-2.8084	4.6054	-2.6299	6.0811	-0.1648	0.368	-0.3208	-0.3079	0.0782	-0.1163	0.3196	-0.043	0.0866	0.1007	-0.0064	0.0011	0.0649	-0.0059	0.078	77.567	21.1585	243.2847
51	2.1654	1.6996	-3.0388	2.784	-3.1755	6.5823	0.0406	0.132	-0.1471	0.0817	0.086	0.1343	-0.2616	-0.1318	-0.1266	0.0659	0.0063	0.0071	0.0793	0.0141	0.0962	69.5942	17.0489	252.9403
52	3.7469	-1.7579	-3.2968	1.5648	0.097	11.5682	0.1443	0.1814	0.2748	-0.0811	-0.0279	0.1748	-0.1686	-0.3081	-0.1164	0.1052	0.0138	-0.0206	0.0886	0.0565	0.274	62.1825	12.4718	263.8389
53	5.3003	1.3016	0.8818	2.7963	-0.1489	1.3716	0.0715	-0.2038	0.2981	0.0821	0.0483	-0.0495	-0.0219	-0.0171	-0.1198	0.0645	-0.0006	0.0217	0.0658	-0.0148	0.1149	60.1063	7.5095	274.6119
54	3.8876	-0.2033	-2.036	3.4539	1.6385	1.7525	-0.017	-0.0694	-0.1761	0.1611	-0.0443	-0.0176	0.0596	0.0302	0.0614	0.1016	0.0123	-0.0295	0.0836	-0.0021	0.0763	72.759	13.3717	274.3816
55	1.4616	1.4589	-2.3619	2.0995	-2.6089	5.8098	-0.0532	-0.0158	-0.2174	0.0781	-0.0092	-0.2598	-0.0028	0.1169	0.0624	0.0447	0.0183	-0.0137	0.0754	-0.0024	0.1272	81.6709	11.206	263.3037
56	3.7405	2.8496	-2.6183	3.7167	-3.2853	3.8115	-0.0879	0.0762	-0.1858	-0.0534	0.0307	-0.2437	0.1046	0.0991	0.0572	0.044	-0.0021	0.0076	0.0788	-0.0141	0.0746	78.3434	7.8103	252.807
57	1.8298	-0.1295	-1.9302	1.0009	-0.5627	3.6218	-0.083	0.0279	-0.1009	-0.0455	-0.0099	-0.1195	0.2155	0.0274	0.0929	0.078	0.0053	-0.0098	0.0509	0.0182	0.0798	66.73	-3.5865	264.1532
58	5.3939	-3.9656	0.1354	9.9579	0.0402	3.2304	-0.1233	0.0157	-0.3764	0.2502	0.0764	-0.0215	0.2781	0.1061	0.0468	0.0826	-0.0144	0.0181	0.0703	0.0085	0.0918	56.657	-6.2696	269.9297
59	0.7135	0.0358	-1.3673	0.5498	0.0942	2.8376	0.0332	0.0816	0.0327	0.0141	0.0496	0.0084	-0.02	-0.1034	-0.0828	0.0586	-0.0034	-0.0014	0.0665	0.0169	0.0755	62.2032	2.1693	257.6842
60	9.3859	4.9687	-3.1295	5.8101	-0.5468	6.932	-0.0677	0.0639	-0.2742	-0.1317	0.0027	-0.1	0.2563	0.1935	0.0651	0.0362	0.0102	0.0025	0.0594	-0.0049	0.058	73.8458	5.3755	244.4438

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 10
2	X-RAY DIFFRACTION	2	A	11 - 20
3	X-RAY DIFFRACTION	3	A	21 - 32
4	X-RAY DIFFRACTION	4	A	33 - 43
5	X-RAY DIFFRACTION	5	A	44 - 54
6	X-RAY DIFFRACTION	6	A	55 - 63
7	X-RAY DIFFRACTION	7	A	64 - 69
8	X-RAY DIFFRACTION	8	A	70 - 79
9	X-RAY DIFFRACTION	9	A	80 - 86
10	X-RAY DIFFRACTION	10	A	87 - 99
11	X-RAY DIFFRACTION	11	A	100 - 113
12	X-RAY DIFFRACTION	12	A	114 - 120
13	X-RAY DIFFRACTION	13	A	121 - 127
14	X-RAY DIFFRACTION	14	A	128 - 147
15	X-RAY DIFFRACTION	15	A	148 - 156
16	X-RAY DIFFRACTION	16	B	-2 - 5
17	X-RAY DIFFRACTION	17	B	6 - 14
18	X-RAY DIFFRACTION	18	B	15 - 22
19	X-RAY DIFFRACTION	19	B	23 - 38
20	X-RAY DIFFRACTION	20	B	39 - 48
21	X-RAY DIFFRACTION	21	B	49 - 60
22	X-RAY DIFFRACTION	22	B	61 - 66
23	X-RAY DIFFRACTION	23	B	67 - 79
24	X-RAY DIFFRACTION	24	B	80 - 89
25	X-RAY DIFFRACTION	25	B	90 - 100
26	X-RAY DIFFRACTION	26	B	101 - 114
27	X-RAY DIFFRACTION	27	B	115 - 126
28	X-RAY DIFFRACTION	28	B	127 - 132
29	X-RAY DIFFRACTION	29	B	133 - 148
30	X-RAY DIFFRACTION	30	B	149 - 156
31	X-RAY DIFFRACTION	31	C	0 - 11
32	X-RAY DIFFRACTION	32	C	12 - 20
33	X-RAY DIFFRACTION	33	C	21 - 37
34	X-RAY DIFFRACTION	34	C	38 - 43
35	X-RAY DIFFRACTION	35	C	44 - 48
36	X-RAY DIFFRACTION	36	C	49 - 57
37	X-RAY DIFFRACTION	37	C	58 - 63
38	X-RAY DIFFRACTION	38	C	64 - 69
39	X-RAY DIFFRACTION	39	C	70 - 79
40	X-RAY DIFFRACTION	40	C	80 - 89
41	X-RAY DIFFRACTION	41	C	90 - 100
42	X-RAY DIFFRACTION	42	C	101 - 118
43	X-RAY DIFFRACTION	43	C	119 - 128
44	X-RAY DIFFRACTION	44	C	129 - 145
45	X-RAY DIFFRACTION	45	C	146 - 156
46	X-RAY DIFFRACTION	46	D	-2 - 5
47	X-RAY DIFFRACTION	47	D	6 - 14
48	X-RAY DIFFRACTION	48	D	15 - 34
49	X-RAY DIFFRACTION	49	D	35 - 42
50	X-RAY DIFFRACTION	50	D	43 - 48
51	X-RAY DIFFRACTION	51	D	49 - 60
52	X-RAY DIFFRACTION	52	D	61 - 66
53	X-RAY DIFFRACTION	53	D	67 - 77
54	X-RAY DIFFRACTION	54	D	78 - 86
55	X-RAY DIFFRACTION	55	D	87 - 98
56	X-RAY DIFFRACTION	56	D	99 - 113
57	X-RAY DIFFRACTION	57	D	114 - 125
58	X-RAY DIFFRACTION	58	D	126 - 132
59	X-RAY DIFFRACTION	59	D	133 - 148
60	X-RAY DIFFRACTION	60	D	149 - 156

-
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