PDB-4a6t: Crystal structure of the omega transaminase from Chromobacterium ...

ID or keywords:

Entry

Database: PDB / ID: 4a6t

Title

Crystal structure of the omega transaminase from Chromobacterium violaceum in complex with PLP

Components

OMEGA TRANSAMINASE

Keywords

TRANSFERASE / PLP-BINDING ENZYME / TRANSAMINASE FOLD TYPE I

Function / homology

Function and homology information

adenosylmethionine-8-amino-7-oxononanoate transaminase activity / pyridoxal phosphate binding / identical protein binding / cytosol
Similarity search - Function

Biological species

CHROMOBACTERIUM VIOLACEUM (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Logan, D.T. / Hakansson, M. / Yengo, K. / Svedendahl Humble, M. / Engelmark Cassimjee, K. / Walse, B. / Abedi, V. / Federsel, H.-J. / Berglund, P.

Citation

Journal: FEBS J. / Year: 2012
Title: Crystal Structures of the Chromobacterium Violaceum Omega-Transaminase Reveal Major Structural Rearrangements Upon Binding of Coenzyme Plp.
Authors: Svedendahl Humble, M. / Engelmark Cassimjee, K. / Hakansson, M. / Kimbung, Y.R. / Walse, B. / Abedi, V. / Federsel, H.-J. / Berglund, P. / Logan, D.T.

History

Deposition	Nov 8, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 1, 2012	Group: Database references
Revision 1.2	Jan 17, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_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	4a6t.cif.gz	764.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4a6t.ent.gz	641.6 KB	Display	PDB format
PDBx/mmJSON format	4a6t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4a6t_validation.pdf.gz	468.7 KB	Display	wwPDB validaton report
Full document	4a6t_full_validation.pdf.gz	483.1 KB	Display
Data in XML	4a6t_validation.xml.gz	73.6 KB	Display
Data in CIF	4a6t_validation.cif.gz	106.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a6/4a6t ftp://data.pdbj.org/pub/pdb/validation_reports/a6/4a6t	HTTPS FTP

-
Related structure data

Related structure data	4a6rSC 4a6uC 4a72C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6snu-2 4a72-2 4ah3-1 6snu-1 4e3q-2 5ghf-d 4brf-d 5kqt-1 4brd-d 3nui-d 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: OMEGA TRANSAMINASE

B: OMEGA TRANSAMINASE

C: OMEGA TRANSAMINASE

D: OMEGA TRANSAMINASE

hetero molecules

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

1

A: OMEGA TRANSAMINASE

B: OMEGA TRANSAMINASE

hetero molecules

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

2

C: OMEGA TRANSAMINASE

D: OMEGA TRANSAMINASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	61.490, 62.320, 119.520
Angle α, β, γ (deg.)	105.44, 90.90, 104.52
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.09338, -0.9666, -0.2386), (-0.9635, -0.1481, 0.2229), (-0.2508, 0.2091, -0.9452)	-37.54, -22.66, 78.32
2	given	(0.9766, 0.1921, -0.09642), (-0.1948, 0.9806, -0.01924), (0.0908, 0.03757, 0.9952)	6.947, 12.18, -54.2
3	given	(0.265, -0.8908, -0.3691), (-0.9351, -0.3309, 0.127), (-0.2353, 0.3115, -0.9207)	-38.99, -44.25, -18.87

#1: Protein	OMEGA TRANSAMINASE / PROBABLE AMINOTRANSFERASE Mass: 51279.293 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHROMOBACTERIUM VIOLACEUM (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7NWG4, beta-alanine-pyruvate transaminase, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1111 / 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: 2.06 Å³/Da / Density % sol: 40.4 % / Description: NONE
Crystal grow	pH: 7.4 Details: DROPS OF 200 UL PROTEIN AT 12 MG/ML MIXED WITH 200 UL OF 0.1 M HEPES PH 7.5, 150-300 MM NACL AND 22.5-27.5% PEG 4000.

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04002
Detector	Type: MARRESEARCH SX-165 / Detector: CCD / Date: May 6, 2011 / Details: MULTILAYER MIRROR, VERTICALLY FOCUSING
Radiation	Monochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.04002 Å / Relative weight: 1
Reflection	Resolution: 1.7→30 Å / Num. obs: 210786 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / B_iso Wilson estimate: 20.05 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 12.7
Reflection shell	Resolution: 1.7→1.79 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.38 / Mean I/σ(I) obs: 3.7 / % possible all: 83.6

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A6R

4a6r

Resolution: 1.8→29.339 Å / SU ML: 0.47 / σ(F): 1.99 / Phase error: 21.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2019	7186	5 %
R_work	0.1647	-	-
obs	0.1666	143706	94.03 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 41.55 Å² / k_sol: 0.389 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.7681 Å²	-0.9275 Å²	0.9118 Å²
2-	-	1.4724 Å²	0.3599 Å²
3-	-	-	-0.7043 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→29.339 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14277	0	60	1111	15448

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	14719
X-RAY DIFFRACTION	f_angle_d	1.008	19933
X-RAY DIFFRACTION	f_dihedral_angle_d	13.536	5315
X-RAY DIFFRACTION	f_chiral_restr	0.058	2069
X-RAY DIFFRACTION	f_plane_restr	0.004	2601

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 (%)
1.8-1.8205	0.3448	211	0.3282	4013	X-RAY DIFFRACTION	84
1.8205-1.8419	0.321	238	0.3043	4530	X-RAY DIFFRACTION	93
1.8419-1.8644	0.3302	239	0.2869	4535	X-RAY DIFFRACTION	94
1.8644-1.888	0.2839	241	0.2631	4573	X-RAY DIFFRACTION	93
1.888-1.9128	0.2722	235	0.2444	4469	X-RAY DIFFRACTION	94
1.9128-1.939	0.2613	240	0.2419	4570	X-RAY DIFFRACTION	94
1.939-1.9667	0.2765	239	0.23	4534	X-RAY DIFFRACTION	94
1.9667-1.996	0.2825	242	0.2259	4594	X-RAY DIFFRACTION	94
1.996-2.0272	0.2411	239	0.2109	4536	X-RAY DIFFRACTION	94
2.0272-2.0605	0.2489	240	0.1946	4575	X-RAY DIFFRACTION	94
2.0605-2.096	0.2142	239	0.1786	4534	X-RAY DIFFRACTION	94
2.096-2.1341	0.2186	240	0.1763	4569	X-RAY DIFFRACTION	94
2.1341-2.1751	0.2108	240	0.1681	4548	X-RAY DIFFRACTION	95
2.1751-2.2195	0.2114	243	0.1582	4616	X-RAY DIFFRACTION	95
2.2195-2.2677	0.2063	239	0.1572	4547	X-RAY DIFFRACTION	94
2.2677-2.3205	0.1878	241	0.1479	4577	X-RAY DIFFRACTION	95
2.3205-2.3785	0.194	241	0.1461	4588	X-RAY DIFFRACTION	94
2.3785-2.4428	0.2008	241	0.1543	4573	X-RAY DIFFRACTION	95
2.4428-2.5146	0.1923	243	0.1485	4605	X-RAY DIFFRACTION	95
2.5146-2.5957	0.1747	243	0.146	4632	X-RAY DIFFRACTION	95
2.5957-2.6884	0.2165	241	0.148	4572	X-RAY DIFFRACTION	95
2.6884-2.796	0.1687	245	0.1437	4660	X-RAY DIFFRACTION	96
2.796-2.9231	0.1952	243	0.1446	4606	X-RAY DIFFRACTION	95
2.9231-3.0771	0.1992	244	0.1469	4639	X-RAY DIFFRACTION	96
3.0771-3.2696	0.191	243	0.1514	4616	X-RAY DIFFRACTION	96
3.2696-3.5217	0.1944	242	0.1523	4594	X-RAY DIFFRACTION	95
3.5217-3.8754	0.1739	241	0.1433	4579	X-RAY DIFFRACTION	94
3.8754-4.4345	0.1534	240	0.1267	4560	X-RAY DIFFRACTION	94
4.4345-5.5807	0.1651	239	0.1445	4539	X-RAY DIFFRACTION	94
5.5807-29.3426	0.1961	234	0.1717	4437	X-RAY DIFFRACTION	92

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	0.4655	0.1781	-0.0871	1.4128	-0.0941	2.7391	0.0525	-0.1231	-0.5095	0.2257	-0.0056	0.2419	0.6065	0.0997	-0.0864	0.328	0.0127	-0.0723	0.2283	0.0486	0.4008	-24.2705	-33.7949	-36.301
2	1.2287	-0.0937	0.8048	1.2825	0.3492	1.6681	0.162	0.1291	-0.3011	-0.0714	0.0007	-0.116	0.3162	0.3201	-0.137	0.2274	0.0966	-0.0198	0.2354	-0.0606	0.2227	-11.9948	-27.6626	-48.2305
3	1.0021	-0.3294	0.2464	1.1744	0.0453	0.8223	0.0039	-0.0261	0.002	0.009	0.0036	-0.2344	-0.0139	0.1683	-0.0115	0.0841	-0.0075	0.0176	0.1684	0.023	0.1254	-21.1342	-4.0088	-46.2493
4	0.8462	0.3074	0.2504	2.4048	0.5519	1.7973	0.0747	0.1236	-0.1001	-0.2617	-0.1379	0.3524	-0.0777	-0.2221	0.0792	0.1295	0.0238	-0.0492	0.2409	0.0056	0.1662	-43.0031	-6.5462	-59.2558
5	1.0461	-0.4699	0.2676	0.8418	-0.0192	0.8846	0.06	0.1817	0.0358	-0.1059	-0.0165	-0.1044	-0.0776	0.1564	-0.0487	0.1225	0.0028	0.0112	0.1935	0.0108	0.0999	-21.7608	-7.4869	-54.8527
6	1.2689	-0.1126	-0.1003	0.8999	0.0309	1.3512	0.0062	0.4414	-0.3535	-0.2732	0.0186	0.2346	0.3618	0.0811	0.0007	0.3118	0.0724	-0.113	0.2473	-0.1367	0.2778	-30.2373	-27.6993	-64.7522
7	2.6234	-0.8158	-0.2466	2.4889	0.171	1.7505	-0.1055	-0.1438	-0.2566	0.1895	-0.0332	0.0937	0.2544	-0.2269	0.1042	0.2749	-0.1085	-0.0522	0.2423	0.0092	0.4604	-44.3029	-29.5487	-51.9504
8	0.3857	-0.3572	-0.0211	0.7741	-0.1081	1.1385	0.1261	0.1555	-0.4014	0.1256	0.0318	0.3728	0.5433	-0.1112	-0.0937	0.3685	-0.0059	-0.1345	0.1857	-0.0922	0.4721	-33.9109	-34.7326	-55.8204
9	0.5119	-0.1515	0.7865	1.0986	-0.7724	1.5106	0.0341	0.3536	0.2408	-0.2924	0.0047	-0.2364	-0.0222	0.3466	-0.0379	0.2288	-0.0169	0.0769	0.4948	0.0011	0.2742	1.5371	-2.4936	-45.0723
10	1.197	0.1143	0.4617	0.9551	0.7473	1.302	0.0479	0.1858	-0.2032	-0.1009	0.0432	-0.1934	0.0599	0.2928	-0.0705	0.1328	0.0705	0.0183	0.308	-0.0405	0.1966	-0.4641	-17.7444	-35.4977
11	0.9456	-0.4226	-0.2326	1.0797	0.2411	0.9772	-0.0137	-0.0483	-0.2583	-0.0481	0.0493	0.1033	0.2218	-0.0268	-0.0242	0.147	-0.0001	0.0057	0.1404	0.0065	0.1747	-23.6755	-20.7658	-30.6708
12	1.6383	-0.4157	0.1444	1.0705	0.3065	2.0913	0.0814	0.4377	0.1729	-0.1028	-0.0351	-0.0006	-0.2381	0.0013	-0.0401	0.0992	0.015	0.0137	0.1789	0.0501	0.1244	-25.7881	0.6431	-29.3743
13	1.767	0.2981	-0.034	0.978	0.0831	1.2088	0.036	0.0168	0.1429	0.0812	-0.0196	0.0229	-0.1246	0.0026	-0.0021	0.1392	0.0149	0.0178	0.1063	0.0115	0.09	-20.8917	3.6107	-14.7601
14	0.4778	-0.0094	0.0638	0.5443	0.1458	0.8383	0.0183	0.0482	-0.0842	0.0794	0.0235	-0.0289	0.0748	0.1221	-0.0378	0.1033	0.018	0.0099	0.1428	0.0171	0.1183	-12.5343	-11.6203	-20.9896
15	3.4729	-1.6275	-1.0292	3.0169	0.7925	2.8058	0.0924	0.4067	0.3224	-0.1276	-0.0065	-0.038	-0.5151	0.0698	-0.084	0.3452	-0.0446	0.0781	0.2606	0.0641	0.2267	-0.5172	12.4922	-24.4577
16	1.4599	-0.2856	-0.1547	2.4096	-0.0733	1.174	0.0705	0.1373	0.2007	0.0118	0.0326	-0.3062	-0.2522	0.3398	-0.0639	0.1173	-0.0643	0.0232	0.3056	0.0191	0.1806	6.0495	2.7123	-23.9864
17	0.2333	-0.1434	0.1946	1.0445	-0.2825	2.2754	-0.0855	-0.2203	-0.1779	0.3246	0.078	0.0691	0.393	0.1597	0.0065	0.2382	0.011	-0.0008	0.1356	0.0504	0.1472	-19.8381	-50.549	21.795
18	0.5671	0.2074	0.1507	1.0271	0.2674	0.6162	-0.0237	0.0282	0.1161	-0.0877	0.0718	-0.1986	-0.0471	0.1305	-0.0435	0.098	0.0053	0.0389	0.0822	0.0077	0.1661	-8.5021	-33.7538	8.5773
19	0.7884	0.0342	0.0646	1.2281	0.1552	0.7656	0.0246	0.0061	0.0543	-0.176	-0.0616	0.0759	-0.1098	-0.0812	0.0275	0.1114	0.0192	0.0006	0.0553	0.0239	0.071	-35.1635	-23.9691	7.0211
20	0.4585	-0.0967	0.0799	0.5211	0.0659	0.4445	0.0328	0.03	0.1028	-0.2142	-0.0015	-0.1027	-0.1566	-0.0101	-0.0062	0.1914	0.0022	0.0313	0.0716	0.0451	0.1195	-22.1328	-24.5094	2.3402
21	1.6917	0.0219	-0.1147	0.8914	0.142	0.8558	0.0197	0.0083	-0.1788	-0.0158	-0.0699	0.1651	0.1223	-0.1255	0.021	0.0927	-0.0227	0.0064	0.0458	-0.0092	0.0923	-32.925	-50.4129	0.9086
22	0.9172	-0.12	0.4887	0.8056	-0.477	1.4534	0.0134	0.1882	0.2975	-0.1939	0.0186	-0.3054	-0.1049	0.2688	-0.0184	0.1811	-0.0516	0.0948	0.1482	-0.0093	0.3125	-1.9791	-15.0649	9.5564
23	0.8241	0.3363	0.0808	0.895	0.4563	0.9372	-0.0033	-0.0701	0.0357	0.1127	0.1025	-0.2081	0.1391	0.159	-0.0821	0.1118	0.039	-0.0174	0.1126	0.0047	0.2036	-6.4067	-35.7079	21.0495
24	1.5502	-0.1168	-0.2193	1.1936	0.3617	1.0278	0.0085	-0.025	0.0883	0.0933	-0.0041	0.0364	0.0155	-0.0388	-0.0072	0.1344	-0.0121	0.0133	0.1137	0.011	0.0899	-26.4961	-23.935	28.9567
25	0.8209	0.1699	-0.0007	0.8982	-0.1078	1.2009	0.0633	-0.3184	0.3119	0.3347	0.0154	-0.1253	-0.1947	0.0915	-0.0438	0.2297	-0.0135	-0.0155	0.1658	-0.0856	0.1647	-22.1123	-12.3351	41.9579
26	0.6267	-0.2962	-0.2398	0.6958	0.4037	1.0415	-0.0617	-0.1916	-0.0096	0.2527	0.1165	-0.0734	0.1684	0.003	-0.0469	0.16	0.0231	-0.026	0.1152	0.0122	0.0862	-17.2046	-30.608	33.5714
27	0.3455	-0.2542	-0.0297	0.6713	-0.0486	0.2251	0.0487	-0.1879	0.2412	0.1816	0.0336	-0.2544	0.0006	0.1201	0.0394	0.1922	0.0107	-0.1633	0.2994	-0.1796	0.4954	1.5683	-15.0355	39.2335
28	2.5949	-0.9065	-0.8178	2.5704	0.8154	1.9809	-0.0733	0.0103	0.2069	0.0457	0.0548	0.0685	-0.2015	-0.0309	0.0285	0.2465	-0.0602	0.0783	0.1425	-0.0904	0.5064	-4.6427	0.1461	29.9382
29	0.872	0.3303	-0.195	0.6574	0.2089	0.5244	0.0746	-0.0063	0.2367	0.026	0.111	-0.2322	-0.1333	0.2043	0.1242	0.1407	-0.0698	-0.0193	0.216	-0.1442	0.4929	3.4373	-8.1553	29.8855

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 5:46)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 47:82)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 83:179)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 180:215)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 216:341)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 342:383)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESSEQ 384:410)
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESSEQ 411:458)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 5:46)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 47:82)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 83:137)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 138:179)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 180:240)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 241:383)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESSEQ 384:411)
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESSEQ 412:458)
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESSEQ 5:46)
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESSEQ 47:106)
19	X-RAY DIFFRACTION	19	CHAIN C AND (RESSEQ 107:238)
20	X-RAY DIFFRACTION	20	CHAIN C AND (RESSEQ 239:341)
21	X-RAY DIFFRACTION	21	CHAIN C AND (RESSEQ 342:458)
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESSEQ 5:46)
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESSEQ 47:106)
24	X-RAY DIFFRACTION	24	CHAIN D AND (RESSEQ 107:179)
25	X-RAY DIFFRACTION	25	CHAIN D AND (RESSEQ 180:240)
26	X-RAY DIFFRACTION	26	CHAIN D AND (RESSEQ 241:341)
27	X-RAY DIFFRACTION	27	CHAIN D AND (RESSEQ 342:383)
28	X-RAY DIFFRACTION	28	CHAIN D AND (RESSEQ 384:411)
29	X-RAY DIFFRACTION	29	CHAIN D AND (RESSEQ 412:458)

-
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