PDB-3wsf: Oxidized HcgD from Methanocaldococcus jannaschii with citrate

ID or keywords:

Entry

Database: PDB / ID: 3wsf

Title

Oxidized HcgD from Methanocaldococcus jannaschii with citrate

Components

Putative GTP cyclohydrolase 1 type 2

Keywords

METAL BINDING PROTEIN / NIF3-related protein

Function / homology

NIF3 (NGG1p interacting factor 3)-like / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / CITRIC ACID / :

Function and homology information

Biological species

Methanocaldococcus jannaschii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Fujishiro, T. / Ermler, U. / Shima, S.

Citation

Journal: Febs Lett. / Year: 2014
Title: A possible iron delivery function of the dinuclear iron center of HcgD in [Fe]-hydrogenase cofactor biosynthesis
Authors: Fujishiro, T. / Ermler, U. / Shima, S.

History

Deposition	Mar 13, 2014	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 27, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3wsf.cif.gz	612.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3wsf.ent.gz	508.1 KB	Display	PDB format
PDBx/mmJSON format	3wsf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3wsf_validation.pdf.gz	470.9 KB	Display	wwPDB validaton report
Full document	3wsf_full_validation.pdf.gz	478 KB	Display
Data in XML	3wsf_validation.xml.gz	65.5 KB	Display
Data in CIF	3wsf_validation.cif.gz	94.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ws/3wsf ftp://data.pdbj.org/pub/pdb/validation_reports/ws/3wsf	HTTPS FTP

-
Related structure data

Related structure data	3wsdC 3wseC 3wsgC 3wshC 3wsiC 2fywS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3wsh-1 3wsg-d 3wsd-d 3wsh-5 3wsh-4 3wsi-d 3wse-d 3wsh-6 3wsh-2 3wsh-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative GTP cyclohydrolase 1 type 2

B: Putative GTP cyclohydrolase 1 type 2

C: Putative GTP cyclohydrolase 1 type 2

D: Putative GTP cyclohydrolase 1 type 2

E: Putative GTP cyclohydrolase 1 type 2

F: Putative GTP cyclohydrolase 1 type 2

hetero molecules

171 kDa, 6 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)	95.190, 137.250, 160.910
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Putative GTP cyclohydrolase 1 type 2 / HcgD / GTP cyclohydrolase I Mass: 28254.553 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSM 2661 / Gene: MJ0927 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1264 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE SEQUENCE HAS ALREADY BEEN DEPOSITED GENBANK, NP_247922. N-TERMINAL RESIDUE, GLY (-2), SER (-1), ...THE SEQUENCE HAS ALREADY BEEN DEPOSITED GENBANK, NP_247922. N-TERMINAL RESIDUE, GLY (-2), SER (-1), HIS(0), ARE THE EXPRESSION TAGS.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.1 Å³/Da / Density % sol: 60.29 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 10%(w/v) PEG4000, 10%(v/v) 2-propanol, 0.1M Sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2012

Radiation

Monochromator: Si(111) monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 141911 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.11 % / B_iso Wilson estimate: 24.37 Å² / R_merge(I) obs: 0.109 / Χ²: 1.034 / Net I/σ(I): 11.08

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2-2.1		0.833	0.735	2.67	77064	19201	19146	0.844	99.7
2.1-2.3		0.431	0.427	4.72	123874	29160	29062	0.485	99.7
2.3-2.8		0.209	0.207	8.42	172732	41564	41424	0.236	99.7
2.8-3.3		0.086	0.093	14.45	82580	20214	20138	0.107	99.6
3.3-4.3		0.044	0.056	20.68	70933	17556	17444	0.064	99.4
4.3-5.9		0.033	0.044	24.65	34123	8981	8849	0.051	98.5
5.9-8		0.031	0.041	26.29	13761	3478	3442	0.047	99
8-12		0.023	0.031	30.3	5926	1688	1655	0.037	98
	12	0.019	0.029	32.66	2874	783	751	0.034	95.9

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.8.4_1496	refinement
PDB_EXTRACT	3.14	data extraction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FYW

2fyw

Resolution: 2→45.778 Å / FOM work R set: 0.8549 / SU ML: 0.24 / σ(F): 1.35 / Phase error: 21.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2145	7111	5.01 %	RANDOM
R_work	0.1777	-	-	-
obs	0.1796	141838	99.5 %	-

Solvent computation

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

Displacement parameters

B_iso max: 80.62 Å² / B_iso mean: 29.73 Å² / B_iso min: 11.06 Å²

Refinement step

Cycle: LAST / Resolution: 2→45.778 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11689	0	84	1264	13037

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11987
X-RAY DIFFRACTION	f_angle_d	1.105	16172
X-RAY DIFFRACTION	f_chiral_restr	0.05	1856
X-RAY DIFFRACTION	f_plane_restr	0.005	2050
X-RAY DIFFRACTION	f_dihedral_angle_d	14.138	4492

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2-2.0227	0.3392	246	0.3034	4452	4698	100
2.0227-2.0465	0.3279	225	0.2811	4455	4680	100
2.0465-2.0714	0.3302	227	0.2631	4477	4704	100
2.0714-2.0977	0.2655	268	0.2465	4375	4643	100
2.0977-2.1253	0.2661	241	0.2226	4472	4713	100
2.1253-2.1544	0.2705	216	0.2145	4466	4682	99
2.1544-2.1852	0.2472	233	0.2118	4434	4667	100
2.1852-2.2178	0.222	260	0.1977	4455	4715	100
2.2178-2.2524	0.2355	238	0.1997	4473	4711	100
2.2524-2.2894	0.2516	252	0.1898	4448	4700	100
2.2894-2.3288	0.2316	205	0.1954	4487	4692	100
2.3288-2.3712	0.2612	225	0.1936	4486	4711	100
2.3712-2.4168	0.2146	229	0.1902	4451	4680	100
2.4168-2.4661	0.2283	245	0.1846	4465	4710	100
2.4661-2.5197	0.2231	224	0.1781	4520	4744	100
2.5197-2.5783	0.2347	226	0.1777	4476	4702	100
2.5783-2.6428	0.2329	212	0.1864	4492	4704	99
2.6428-2.7143	0.2201	227	0.1804	4463	4690	100
2.7143-2.7941	0.2289	252	0.1848	4492	4744	100
2.7941-2.8843	0.2381	232	0.1905	4478	4710	100
2.8843-2.9874	0.2167	231	0.1734	4507	4738	100
2.9874-3.1069	0.2248	242	0.1776	4467	4709	100
3.1069-3.2483	0.209	218	0.1771	4520	4738	100
3.2483-3.4195	0.2255	242	0.1766	4535	4777	99
3.4195-3.6337	0.1983	281	0.1772	4467	4748	100
3.6337-3.9141	0.1991	230	0.1585	4533	4763	99
3.9141-4.3077	0.1646	231	0.141	4544	4775	99
4.3077-4.9304	0.1473	242	0.1266	4496	4738	98
4.9304-6.2094	0.2048	273	0.159	4569	4842	99
6.2094-45.7897	0.1802	238	0.1627	4772	5010	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	2.9297	-0.4909	0.4028	2.7075	-0.2606	1.8083	0.0713	-0.0471	-0.3444	-0.025	0.0442	0.1682	0.2682	-0.2733	-0.1004	0.1471	-0.0352	-0.01	0.1661	-0.0062	0.157	-11.8493	-113.7966	-72.3971
2	1.1247	-1.2691	-0.6054	3.5256	0.2691	1.2967	0.0397	-0.1717	0.1048	0.0519	0.0284	-0.0516	0.0537	-0.1277	-0.0835	0.1578	-0.0055	-0.0024	0.2094	-0.0154	0.1794	-11.8436	-101.6121	-67.9555
3	3.219	0.1455	0.1598	1.2736	0.5966	1.7937	0.0998	0.0647	-0.6915	0.0063	0.1804	-0.2267	0.4464	0.1466	-0.2239	0.2587	0.0681	-0.0808	0.1267	-0.0753	0.3506	13.4236	-120.6775	-69.3395
4	3.5476	0.6911	1.7547	0.6237	0.4094	1.6084	0.1393	0.136	-0.2917	0.0566	0.0022	-0.1031	0.1748	0.0954	-0.0961	0.1857	0.0251	-0.0126	0.1198	-0.0459	0.2007	12.912	-112.1599	-69.5747
5	1.4225	-0.2779	-0.1856	2.8229	0.9106	2.8126	0.0111	0.039	0.335	-0.013	0.1058	-0.2374	-0.3488	0.3518	-0.1186	0.2259	-0.0886	0.0362	0.2166	-0.0397	0.2463	-19.1948	-79.7074	-57.9921
6	3.3869	0.2016	-0.8067	2.6281	-0.6583	1.7274	0.1694	0.304	0.218	-0.1893	-0.0186	-0.1043	-0.3725	0.1697	-0.0918	0.2508	-0.0351	0.0133	0.199	-0.0232	0.1579	-26.014	-85.0849	-66.2857
7	3.0395	0.4664	0.3552	4.1071	-1.6257	3.5117	-0.0768	0.1722	-0.0786	-0.1529	0.151	0.1285	0.0077	-0.249	-0.0107	0.1482	0.0015	0.0114	0.1956	-0.0511	0.1622	-31.5522	-90.9932	-64.7483
8	1.9139	-1.2125	-0.8839	3.4531	1.2034	1.1281	-0.0048	-0.0047	0.0553	0.0642	0.0693	-0.0372	0.0665	0.2376	-0.0634	0.1606	-0.0235	0.0092	0.2084	-0.0124	0.1332	-21.3718	-95.9311	-61.4404
9	2.5758	-0.3638	-0.688	1.2822	-0.6617	2.9755	-0.0072	-0.272	0.3868	0.2155	0.1547	0.1384	-0.5932	-0.0341	-0.1236	0.3129	0.0393	0.0212	0.1499	-0.0498	0.2233	-32.1688	-77.193	-38.1344
10	1.556	-0.1714	0.3136	2.4751	-0.9267	1.9198	-0.0846	-0.2716	0.0898	0.3196	0.164	0.1791	-0.1722	-0.1382	-0.0427	0.2872	0.0357	0.025	0.2547	-0.0104	0.1839	-35.511	-85.1713	-31.9297
11	2.9885	0.0472	-0.6888	4.9818	1.1763	2.6973	0.0489	-0.3399	0.0168	0.1188	0.0268	-0.2745	-0.1351	0.1586	-0.0382	0.2248	0.0259	0.0031	0.2212	-0.0106	0.1413	-26.7663	-87.4803	-31.1015
12	1.1282	-0.1601	0.6064	1.6072	-0.449	2.6564	-0.0292	-0.3038	-0.1841	0.1836	0.1418	0.0277	0.0459	-0.0075	-0.0314	0.2116	0.0282	0.0107	0.2423	0.0234	0.1669	-31.132	-93.2174	-28.7301
13	1.2447	0.3865	-0.2228	2.0928	-0.2115	1.6583	0.0191	0.027	0.0902	-0.1154	-0.0518	0.1281	-0.1626	0.0201	0.0415	0.2092	0.0252	0.021	0.1651	-0.0123	0.1682	-34.2836	-80.7143	-55.8372
14	2.5977	0.9662	0.6373	2.77	0.2347	1.4729	-0.0745	0.0003	0.2652	0.0281	0.014	0.1628	-0.1349	-0.2627	0.0557	0.149	0.0281	0.0061	0.2671	0.0473	0.1894	-7.9438	-88.7156	-9.4055
15	3.5777	0.0571	1.2765	0.9354	0.4351	2.4837	-0.0519	0.2185	0.3702	-0.1678	0.05	-0.0572	-0.2992	-0.0096	-0.0115	0.2836	0.0207	-0.0075	0.1852	0.0816	0.2817	12.5119	-77.3325	-16.6837
16	1.9356	-0.9772	-0.0781	2.2138	1.2429	2.7996	-0.0251	0.1797	0.0662	0.0593	-0.0083	-0.1227	-0.1427	0.1249	0.0328	0.1698	-0.0172	-0.0007	0.167	0.049	0.1897	23.5872	-87.1283	-15.8254
17	2.0378	-0.1542	-0.5102	2.3606	-0.1427	0.9869	0.0009	0.0166	0.1765	0.1759	-0.0454	0.0354	-0.2095	-0.0634	0.06	0.1593	0.0136	-0.0243	0.1456	0.0147	0.146	3.1573	-81.5647	-2.8591
18	1.3573	-0.553	0.129	2.1625	0.2795	2.5697	-0.0663	-0.2545	-0.2112	0.1505	0.0325	0.0109	0.263	0.0484	0.0087	0.1676	-0.0246	0.0042	0.2629	0.048	0.168	-23.4298	-113.2331	-15.1185
19	1.5546	1.3085	0.4328	3.185	1.4767	0.3542	-0.0693	-0.0795	-0.0071	-0.0459	0.036	-0.0076	0.06	0.0997	0.0613	0.188	-0.0094	0.009	0.3272	0.0564	0.1746	-19.3104	-101.411	-16.7562
20	3.616	0.0144	1.3886	1.363	-0.332	2.5754	0.1964	0.0727	-0.2691	-0.2873	0.0727	0.0602	0.6165	-0.1185	-0.2032	0.3994	-0.0743	0.0147	0.2577	0.006	0.2815	-28.1718	-120.6335	-36.4532
21	2.0297	-0.2532	-0.2351	2.6593	-1.5322	3.6691	-0.1438	0.1011	-0.264	-0.2169	0.1019	0.048	0.317	-0.4314	0.04	0.1965	-0.0796	0.0231	0.2249	-0.0315	0.1838	-35.1408	-110.8328	-45.1607
22	1.0391	-0.8572	0.8	1.703	-0.5834	2.1064	0.0875	-0.2046	-0.2506	0.1267	-0.0128	0.1089	0.2727	-0.348	-0.0668	0.2293	-0.0919	0.0114	0.3554	0.0315	0.2677	-33.7835	-115.6872	-20.8458
23	2.138	0.8409	-0.9259	2.7411	-0.4021	2.9246	-0.2482	0.0568	-0.443	-0.1583	0.1075	-0.1862	0.4857	0.1356	0.1079	0.2666	0.0166	0.0218	0.2132	0.0147	0.252	30.3274	-115.1143	-33.8697
24	1.0554	-0.0724	0.2436	3.2506	-0.8241	2.3938	-0.0279	0.0036	-0.0659	0.0466	0.0639	-0.0656	0.0512	0.1263	-0.0291	0.1564	-0.0133	-0.0065	0.2245	0.0065	0.1697	29.6051	-104.5147	-35.0565
25	3.0248	-0.8137	-1.3686	1.3947	0.8067	2.6927	-0.2475	-0.4232	-0.5224	0.2222	0.0212	0.1151	0.4353	0.1975	0.1663	0.2922	0.0191	0.0402	0.2291	0.1534	0.2759	13.5583	-116.1564	-10.975
26	1.7111	0.3825	-1.2936	0.0523	0.2587	1.5422	-0.1476	-0.2059	-0.264	0.0398	0.0573	-0.0504	0.2316	0.1982	0.0638	0.2727	0.0428	0.0022	0.2533	0.1024	0.2553	23.1618	-112.6662	-16.9278
27	1.4644	-0.7989	0.0708	3.5836	-0.3029	2.6784	0.0009	-0.221	0.2494	0.4118	-0.0968	-0.356	-0.4922	0.1479	0.0837	0.23	-0.0443	-0.0452	0.1697	-0.0172	0.2061	28.8667	-82.8707	-48.3162
28	4.3323	0.6856	0.0215	5.147	1.6936	2.8599	0.085	0.0331	-0.0011	-0.1188	-0.0185	-0.4277	-0.0464	0.3984	-0.0744	0.1393	-0.0132	-0.0052	0.2095	0.0364	0.1643	35.8917	-92.997	-54.8352
29	0.5192	-0.3024	-0.2728	2.909	-1.9475	1.4811	0.0293	-0.1961	-0.0085	-0.084	-0.0189	0.0066	0.1163	0.0007	-0.0157	0.1908	-0.0154	-0.0265	0.1865	-0.0011	0.1678	27.4926	-97.3486	-47.7994
30	1.6103	0.1189	0.1591	0.6943	-0.8101	4.2721	0.0016	-0.0387	0.3624	0.0651	-0.0304	0.035	-0.3675	-0.1254	-0.0036	0.2323	0.0296	-0.0012	0.1142	-0.0433	0.3161	13.6638	-77.4268	-63.196
31	3.1037	1.1861	-0.3204	2.3173	-0.2317	1.6522	0.064	0.127	0.1399	-0.0787	-0.0368	0.07	-0.0037	-0.1178	-0.0231	0.1455	0.0395	-0.0056	0.1139	-0.0242	0.1706	8.6713	-86.736	-73.6444
32	1.0402	0.202	1.1404	2.0434	0.4032	1.2276	0.0413	-0.0364	0.141	-0.0467	-0.1541	-0.1591	-0.1788	0.1518	0.0759	0.1979	-0.0308	0.0048	0.1758	0.0288	0.2301	30.0836	-82.4279	-61.9201

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 2:69 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 70:103 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 104:154 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 155:249 )
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESSEQ 6:34 )
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 35:52 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 53:69 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 70:103 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 104:154 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 155:182 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 183:202 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 203:220 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 221:249 )
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESSEQ 5:103 )
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESSEQ 104:135 )
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESSEQ 136:220 )
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESSEQ 221:249 )
18	X-RAY DIFFRACTION	18	CHAIN D AND (RESSEQ 3:69 )
19	X-RAY DIFFRACTION	19	CHAIN D AND (RESSEQ 70:103 )
20	X-RAY DIFFRACTION	20	CHAIN D AND (RESSEQ 104:135 )
21	X-RAY DIFFRACTION	21	CHAIN D AND (RESSEQ 136:220 )
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESSEQ 221:249 )
23	X-RAY DIFFRACTION	23	CHAIN E AND (RESSEQ 4:61 )
24	X-RAY DIFFRACTION	24	CHAIN E AND (RESSEQ 62:103 )
25	X-RAY DIFFRACTION	25	CHAIN E AND (RESSEQ 104:202 )
26	X-RAY DIFFRACTION	26	CHAIN E AND (RESSEQ 203:249 )
27	X-RAY DIFFRACTION	27	CHAIN F AND (RESSEQ 4:52 )
28	X-RAY DIFFRACTION	28	CHAIN F AND (RESSEQ 53:69 )
29	X-RAY DIFFRACTION	29	CHAIN F AND (RESSEQ 70:103 )
30	X-RAY DIFFRACTION	30	CHAIN F AND (RESSEQ 104:135 )
31	X-RAY DIFFRACTION	31	CHAIN F AND (RESSEQ 136:220 )
32	X-RAY DIFFRACTION	32	CHAIN F AND (RESSEQ 221:249 )

-
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://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