PDB-6c8t: The structure of MppP soaked with the substrate L-Arg

ID or keywords:

Entry

Database: PDB / ID: 6c8t

Title

The structure of MppP soaked with the substrate L-Arg

Components

(PLP-Dependent L-Arginine Hydroxylase MppP) x 2

Keywords

OXIDOREDUCTASE / dimer / L-Arg binding complex / oxidase / PLP / ANTIBIOTIC

Function / homology

Function and homology information

amino acid metabolic process / transaminase activity / biosynthetic process / pyridoxal phosphate binding / metal ion binding
Similarity search - Function

Biological species

Streptomyces wadayamensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Han, L. / Silvaggi, N.R.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2018
Title: Streptomyces wadayamensis MppP is a PLP-Dependent Oxidase, Not an Oxygenase.
Authors: Han, L. / Vuksanovic, N. / Oehm, S.A. / Fenske, T.G. / Schwabacher, A.W. / Silvaggi, N.R.

History

Deposition	Jan 25, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 5, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 4, 2023	Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6c8t.cif.gz	828.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6c8t.ent.gz	699.9 KB	Display	PDB format
PDBx/mmJSON format	6c8t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c8/6c8t ftp://data.pdbj.org/pub/pdb/validation_reports/c8/6c8t	HTTPS FTP

-
Related structure data

Related structure data	5bk7C 6c92C 6c9bC 5dj1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5bk7-2 5bk7-1 5dj3-2 4i8a-1 1j04-2 6nfy-d 5luc-1 6pp9-d 7m0t-d 5ofy-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) 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: PLP-Dependent L-Arginine Hydroxylase MppP

B: PLP-Dependent L-Arginine Hydroxylase MppP

C: PLP-Dependent L-Arginine Hydroxylase MppP

D: PLP-Dependent L-Arginine Hydroxylase MppP

hetero molecules

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

1

A: PLP-Dependent L-Arginine Hydroxylase MppP

B: PLP-Dependent L-Arginine Hydroxylase MppP

hetero molecules

defined by author&software
Evidence: gel filtration
83.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: PLP-Dependent L-Arginine Hydroxylase MppP

D: PLP-Dependent L-Arginine Hydroxylase MppP

hetero molecules

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

Unit cell

Length a, b, c (Å)	85.792, 108.425, 196.219
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	PLP-Dependent L-Arginine Hydroxylase MppP Mass: 41537.750 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces wadayamensis (bacteria) / Plasmid: pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0X1KHF5
#2: Protein	PLP-Dependent L-Arginine Hydroxylase MppP Mass: 41765.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces wadayamensis (bacteria) / Plasmid: pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0X1KHF5
#3: Chemical	ChemComp-EQJ / (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine Mass: 403.328 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₄H₂₂N₅O₇P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 728 / 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: 2.74 Å³/Da / Density % sol: 55.15 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30% polyethylene glycol monomethyl ether 550, 50 mM MgCl2, and 0.1 M HEPES pH 8.0

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 85820 / % possible obs: 91.6 % / Redundancy: 4.8 % / R_merge(I) obs: 0.057 / Net I/σ(I): 24.7
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.193 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 3839 / % possible all: 84.1

-
Processing

Software

Name	Version	Classification
HKL-2000	(1.11.1_2575: ???)	data reduction
HKL-2000		data scaling
PHASER		phasing
PHENIX		refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5DJ1

5dj1

Resolution: 2.2→49.055 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.15

	R_factor	Num. reflection	% reflection
R_free	0.1954	1999	2.33 %
R_work	0.1464	-	-
obs	0.1475	85722	91.56 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.2→49.055 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11331	0	82	728	12141

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	11707
X-RAY DIFFRACTION	f_angle_d	1.119	15954
X-RAY DIFFRACTION	f_dihedral_angle_d	19.826	6967
X-RAY DIFFRACTION	f_chiral_restr	0.067	1806
X-RAY DIFFRACTION	f_plane_restr	0.007	2098

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 (%)
2.1991-2.2541	0.1957	128	0.1432	5359	X-RAY DIFFRACTION	84
2.2541-2.315	0.2083	127	0.1455	5342	X-RAY DIFFRACTION	83
2.315-2.3832	0.2003	130	0.1447	5395	X-RAY DIFFRACTION	83
2.3832-2.4601	0.2154	129	0.1393	5418	X-RAY DIFFRACTION	84
2.4601-2.548	0.2192	132	0.1479	5534	X-RAY DIFFRACTION	85
2.548-2.65	0.1728	134	0.145	5610	X-RAY DIFFRACTION	87
2.65-2.7706	0.2057	140	0.1505	5834	X-RAY DIFFRACTION	90
2.7706-2.9167	0.2144	143	0.1497	6014	X-RAY DIFFRACTION	93
2.9167-3.0994	0.2065	149	0.1448	6247	X-RAY DIFFRACTION	96
3.0994-3.3386	0.1825	153	0.1433	6389	X-RAY DIFFRACTION	98
3.3386-3.6745	0.1729	154	0.1298	6484	X-RAY DIFFRACTION	99
3.6745-4.206	0.1768	158	0.1275	6587	X-RAY DIFFRACTION	100
4.206-5.2981	0.1677	158	0.1368	6632	X-RAY DIFFRACTION	100
5.2981-49.0669	0.244	164	0.1919	6878	X-RAY DIFFRACTION	100

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	0.6486	-0.0212	-0.3659	0.5351	0.0735	1.0672	0.0572	-0.0267	-0.2059	-0.1443	-0.021	-0.0933	0.1831	-0.1558	-0.0514	0.3156	0.0001	0.0296	0.1692	0.0528	0.2786	34.6123	203.3826	223.9368
2	0.8342	0.2045	-0.1714	0.2998	-0.3133	0.3995	0.0135	-0.2325	0.0818	0.1088	-0.0669	-0.0918	-0.0139	0.0906	0.0274	0.1811	0.0006	0.0063	0.1838	0.0245	0.1983	42.1009	220.6173	233.9846
3	1.4353	-0.0832	-0.3453	0.5518	0.2325	0.7094	-0.0884	0.0717	-0.0442	-0.1629	0.0031	-0.0544	0.0428	0.0728	0.0786	0.1954	0.0221	0.0462	0.1455	0.0303	0.1529	45.4688	222.0712	209.4389
4	0.8037	-0.0696	0.0625	1.0979	-0.0003	0.6207	-0.0105	-0.0687	0.0065	-0.0294	0.0002	-0.2271	0.0446	0.1824	0.0039	0.1396	0.0271	0.034	0.1735	0.046	0.2664	54.9982	222.4828	218.5178
5	0.5462	0.6263	-0.3543	2.7281	-0.9789	0.5494	-0.0706	-0.1518	-0.0408	-0.0349	-0.0101	-0.1131	0.0987	0.0748	0.0589	0.1548	0.0019	0.0321	0.1261	0.0489	0.218	41.1459	218.4555	224.8911
6	1.2835	-0.3407	-0.0152	0.6826	0.0287	0.5596	-0.0862	-0.2271	-0.0458	0.1028	0.1038	-0.065	0.0509	-0.0751	-0.0273	0.1562	0.0088	-0.0116	0.1526	0.0376	0.154	36.5596	217.0441	231.1494
7	0.5086	-0.0974	-0.4298	0.6708	0.8678	2.1692	-0.1195	-0.0734	-0.2559	0.0051	-0.0059	-0.2784	0.2461	0.125	-0.0152	0.3382	0.0954	0.0445	0.1605	0.0904	0.4346	52.5051	196.3085	223.034
8	1.6383	-0.4649	-0.0648	2.2325	0.4508	0.634	-0.0309	0.0817	-0.1466	-0.1921	0.1006	-0.3478	0.1186	0.1736	-0.1408	0.3668	0.1272	0.124	0.183	0.0091	0.4332	55.9413	198.639	211.0872
9	0.2746	0.0867	-0.0411	0.9143	0.1104	0.3054	-0.0467	0.2494	-0.1741	-0.5304	0.0123	-0.1133	0.2249	0.0168	-0.023	0.5508	0.0653	0.1185	0.1898	-0.0951	0.3261	45.1157	200.6096	201.6065
10	0.5468	-0.1597	-0.0058	1.2593	0.4907	1.188	-0.0325	0.0272	-0.3219	-0.0658	0.0328	-0.0332	0.3211	0.0866	-0.0327	0.4462	0.0746	0.1033	0.1177	0.0105	0.4631	46.55	191.6525	211.968
11	1.3194	0.7884	-0.0736	1.8292	-0.013	0.7824	-0.0573	-0.1791	-0.0813	-0.0507	0.0032	-0.402	-0.0108	-0.049	-0.0061	0.2094	0.0483	0.0045	0.3168	0.0318	0.2392	23.7312	227.889	234.2271
12	0.8115	-0.5248	0.2005	0.6156	0.0229	0.4797	0.0029	-0.0465	-0.3223	0.0113	-0.0419	-0.0149	0.2956	-0.0703	0.0504	0.2758	-0.0822	-0.0019	0.1631	0.0676	0.2549	20.646	201.9829	226.5122
13	1.3977	0.1851	-0.1134	0.8238	-0.0588	0.7963	0.1498	0.2319	-0.062	-0.1512	-0.091	-0.0466	0.1741	-0.1281	-0.0434	0.2002	-0.0009	-0.022	0.1425	0.0084	0.1636	20.8085	215.604	212.7474
14	1.9787	-0.5745	-0.5253	0.9189	0.6986	0.7799	0.0555	0.0437	0.219	-0.2366	-0.0469	-0.1027	-0.1008	-0.133	0.0155	0.2116	0.0679	0.025	0.2201	0.0509	0.178	20.7399	232.3335	212.9495
15	1.5399	-0.2402	0.3649	0.3568	0.0519	0.326	0.0421	0.3273	0.3889	-0.2045	-0.1384	-0.1043	-0.1237	-0.1166	0.0262	0.265	0.0953	0.0053	0.2796	0.0713	0.1946	12.1976	233.496	207.9775
16	0.9617	0.1856	-0.3334	0.7711	0.0135	1.1467	0.1165	0.0177	-0.0803	-0.1597	-0.0867	0.075	0.0266	-0.3354	-0.0094	0.1718	0.0146	-0.0346	0.2464	-0.0019	0.1603	8.2759	221.7517	211.9692
17	0.6837	-0.1219	-0.2157	0.7848	-0.7641	3.7358	0.005	-0.0145	-0.1389	0.0028	-0.0384	-0.0056	-0.0546	-0.1959	-0.007	0.1999	0.0108	0.0006	0.1537	0.0257	0.155	19.8536	215.3626	217.9686
18	0.7854	-0.35	-0.1007	0.544	0.0008	0.8897	-0.0126	-0.0751	-0.256	-0.094	-0.0476	-0.0306	0.2527	-0.1763	0.0764	0.2486	-0.0722	-0.0198	0.1578	0.0228	0.1958	22.7599	208.8132	220.5067
19	0.9218	0.238	0.4631	4.5021	0.5011	0.7249	-0.038	-0.1947	0.0149	0.2776	0.0255	0.1389	0.0895	-0.3423	0.0452	0.1924	-0.0211	0.0412	0.4589	0.0294	0.1807	5.5279	222.8133	237.1533
20	2.1333	-0.8806	-0.2589	4.297	0.6321	2.1695	0.0305	-0.2205	0.1615	0.3329	-0.0231	0.3185	-0.112	-0.3233	0.0214	0.1654	0.0758	0.0407	0.3323	-0.0312	0.21	5.6345	234.6905	233.0387
21	0.7496	-0.1956	0.1622	1.0755	-0.2804	1.849	-0.0333	-0.1825	0.3612	0.1529	-0.1156	-0.0506	-0.6276	0.055	0.063	0.295	0.0226	-0.0246	0.2564	-0.0691	0.284	18.611	241.029	232.5332
22	1.5792	0.0974	-0.0818	2.0703	-0.0623	2.598	-0.0032	-0.6651	0.1856	0.2605	0.0179	0.14	-0.2403	-0.1096	0.019	0.2334	0.0638	-0.0137	0.4188	-0.0578	0.2014	13.0922	232.8385	241.7402
23	0.4107	-0.0941	-0.4637	0.0904	-0.0676	0.9533	-0.1305	-0.0784	0.1616	-0.0732	0.0859	-0.1807	-0.0358	0.2789	0.0286	0.3885	0.0611	-0.0021	0.3266	-0.0783	0.3685	52.2661	273.4688	212.6367
24	1.2296	-0.2404	0.4131	0.5153	0.3393	0.511	-0.0619	-0.3518	-0.0275	0.1287	0.1059	-0.0216	-0.0467	-0.0225	0.0129	0.273	0.1357	-0.0092	0.3719	-0.093	0.1404	50.2824	261.1553	236.5918
25	1.2714	-0.4965	-0.3252	0.703	0.4125	0.4902	-0.0699	-0.2011	-0.1486	0.077	0.1014	0.08	0.0271	-0.1284	0.0083	0.1338	0.0436	0.0054	0.1948	0.0077	0.1519	46.8085	250.4249	220.7476
26	1.3219	-0.5613	0.1672	0.6531	-0.2937	0.4368	-0.0469	0.0259	0.1005	-0.0985	0.0689	-0.1368	-0.052	0.0171	-0.0291	0.1474	0.0086	-0.0154	0.1434	-0.0122	0.1345	45.2438	253.8655	204.598
27	0.1631	-0.0821	-0.0444	0.991	0.0551	0.8901	-0.0555	-0.2023	-0.0011	0.0098	0.131	0.2743	-0.0199	-0.3337	-0.0143	0.1109	0.058	0.0099	0.2481	0.0109	0.1942	33.5044	253.0698	212.865
28	0.4426	0.4269	0.4062	3.1112	1.5605	0.9404	-0.1017	-0.262	0.0241	0.1641	0.0743	0.0677	-0.0372	-0.1691	0.0614	0.1672	0.0728	0.0046	0.2278	-0.0385	0.1833	46.6913	255.9122	222.21
29	0.6537	-0.109	-0.0279	0.7262	0.4403	0.5074	-0.1161	-0.377	-0.0282	0.1015	0.1272	0.0107	-0.1255	-0.0787	-0.0426	0.2279	0.1004	0.0091	0.2616	-0.0528	0.1187	50.617	256.6982	229.0109
30	0.1317	0.1569	0.0059	0.3681	-0.5327	1.6368	-0.0769	-0.1154	0.081	0.1012	0.0648	0.1342	-0.2168	-0.0903	-0.1218	0.3632	0.1811	-0.0149	0.2535	-0.1142	0.3129	35.5089	278.6652	220.3847
31	1.2885	-0.4606	-0.1331	1.5717	-0.016	0.6657	0.0044	0.0292	0.0514	-0.0591	0.0172	0.1646	-0.1483	-0.0868	-0.0358	0.3833	0.1758	-0.0928	0.207	-0.0759	0.3089	33.2782	276.3921	208.7697
32	0.3725	0.7853	0.0814	2.2598	0.3757	0.7549	0.0628	0.252	0.1803	-0.6124	0.2145	-0.2966	-0.5163	-0.0719	-0.1004	0.4009	0.0327	0.0818	0.1769	0.0278	0.3008	44.8001	275.6552	200.2412
33	0.5415	-0.2655	0.1131	1.4907	-0.3495	0.9133	0.0124	-0.0991	0.2702	-0.0133	0.1494	-0.1038	-0.3396	-0.096	0.0259	0.4222	0.1181	0.0355	0.1349	-0.0455	0.3487	42.5716	283.6692	211.0816
34	1.0736	-1.0976	0.3175	1.5972	0.013	0.7011	-0.1618	-0.3316	0.0865	0.091	0.1168	0.1445	-0.1461	0.1359	0.0716	0.2653	0.0421	0.0192	0.3538	-0.1292	0.206	65.0195	262.6936	234.9996
35	1.0211	-0.2671	-0.2135	0.6276	0.223	0.8459	-0.025	-0.1159	0.0946	-0.0393	0.0035	-0.0429	-0.1153	0.1645	0.029	0.1477	-0.0228	0.0063	0.1608	-0.021	0.1368	72.751	255.1265	214.154
36	0.7495	0.1603	0.1091	1.9837	0.7035	0.7912	-0.0302	-0.4167	-0.105	0.2296	0.0432	-0.1782	0.0543	0.1995	0.003	0.1529	0.0504	-0.0346	0.4613	0.0298	0.1629	81.0166	243.8805	235.1371
37	0.544	0.0669	-0.2104	1.1406	0.2038	1.222	0.1228	-0.4948	-0.2788	0.2184	-0.0822	-0.0596	0.201	-0.2776	-0.0486	0.2309	0.0032	0.007	0.4668	0.1449	0.2605	70.1792	235.0326	234.5425

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 54 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 55 through 89 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 90 through 139 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 140 through 218 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 219 through 242 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 243 through 272 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 273 through 291 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 292 through 313 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 314 through 349 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 350 through 375 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 8 through 35 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 36 through 71 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 72 through 103 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 104 through 124 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 125 through 156 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 157 through 218 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 219 through 242 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 243 through 272 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 273 through 291 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 292 through 313 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 314 through 349 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 350 through 375 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 8 through 35 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 36 through 72 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 73 through 103 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 104 through 127 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 128 through 218 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 219 through 242 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 243 through 272 )
30	X-RAY DIFFRACTION	30	chain 'C' and (resid 273 through 292 )
31	X-RAY DIFFRACTION	31	chain 'C' and (resid 293 through 313 )
32	X-RAY DIFFRACTION	32	chain 'C' and (resid 314 through 349 )
33	X-RAY DIFFRACTION	33	chain 'C' and (resid 350 through 375 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 22 through 54 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 55 through 272 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 273 through 313 )
37	X-RAY DIFFRACTION	37	chain 'D' and (resid 314 through 375 )

-
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

-
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