PDB-5j33: Isopropylmalate dehydrogenase in complex with NAD+

ID or keywords:

Entry

Database: PDB / ID: 5j33

Title

Isopropylmalate dehydrogenase in complex with NAD+

Components

3-isopropylmalate dehydrogenase 2, chloroplastic

Keywords

OXIDOREDUCTASE / dehydrogenase / leucine biosynthesis / glucosinolate biosynthesis

Function / homology

Function and homology information

embryo sac development / 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / pollen development / L-leucine biosynthetic process / chloroplast envelope / chloroplast stroma / plastid / NAD+ binding / chloroplast ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.492 Å

Authors

Jez, J.M. / Lee, S.G.

Citation

Journal: J.Biol.Chem. / Year: 2016
Title: Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: INSIGHTS ON LEUCINE AND ALIPHATIC GLUCOSINOLATE BIOSYNTHESIS.
Authors: Lee, S.G. / Nwumeh, R. / Jez, J.M.

History

Deposition	Mar 30, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 18, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jul 6, 2016	Group: Database references
Revision 1.2	Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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_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.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_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5j33.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb5j33.ent.gz	911.4 KB	Display	PDB format
PDBx/mmJSON format	5j33.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5j33_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	5j33_full_validation.pdf.gz	3.1 MB	Display
Data in XML	5j33_validation.xml.gz	108.5 KB	Display
Data in CIF	5j33_validation.cif.gz	141.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j3/5j33 ftp://data.pdbj.org/pub/pdb/validation_reports/j3/5j33	HTTPS FTP

-
Related structure data

Related structure data	5j32C 5j34C 3r8wS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6kdy-1 4xxv-d 5t49-d 6a5n-d 6kdy-2 2hrc-d 6ke3-1 2aeq-d 4bi9-2 6ke3-2 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

5j32C

5j34C

3r8wS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (5) #154 - Oct 2012 Citric Acid Cycle similarity (5)

Deposited unit

A: 3-isopropylmalate dehydrogenase 2, chloroplastic

B: 3-isopropylmalate dehydrogenase 2, chloroplastic

C: 3-isopropylmalate dehydrogenase 2, chloroplastic

D: 3-isopropylmalate dehydrogenase 2, chloroplastic

E: 3-isopropylmalate dehydrogenase 2, chloroplastic

F: 3-isopropylmalate dehydrogenase 2, chloroplastic

G: 3-isopropylmalate dehydrogenase 2, chloroplastic

H: 3-isopropylmalate dehydrogenase 2, chloroplastic

hetero molecules

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

1

A: 3-isopropylmalate dehydrogenase 2, chloroplastic

B: 3-isopropylmalate dehydrogenase 2, chloroplastic

hetero molecules

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

2

C: 3-isopropylmalate dehydrogenase 2, chloroplastic

H: 3-isopropylmalate dehydrogenase 2, chloroplastic

hetero molecules

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

3

D: 3-isopropylmalate dehydrogenase 2, chloroplastic

F: 3-isopropylmalate dehydrogenase 2, chloroplastic

hetero molecules

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

4

E: 3-isopropylmalate dehydrogenase 2, chloroplastic

G: 3-isopropylmalate dehydrogenase 2, chloroplastic

hetero molecules

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

Unit cell

Length a, b, c (Å)	77.200, 132.868, 349.426
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	3-isopropylmalate dehydrogenase 2, chloroplastic / IMDH 2 / Beta-IPM dehydrogenase 2 Mass: 43420.668 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: IMDH2, IMDH, At1g80560, T21F11.11 / Production host: Escherichia coli (E. coli) References: UniProt: P93832, 3-isopropylmalate dehydrogenase
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.58 Å³/Da / Density % sol: 52.32 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.25 M ammonium sulfate, 0.1 M HEPES, pH7.5, and 5 mM NAD+

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 3.49→46.73 Å / Num. obs: 45923 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.65 % / R_sym value: 0.244 / Net I/σ(I): 6.4
Reflection shell	Resolution: 3.49→3.56 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.776 / Mean I/σ(I) obs: 2 / % possible all: 58.6

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3R8W

3r8w

Resolution: 3.492→46.729 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2608	2317	5.08 %
R_work	0.1891	-	-
obs	0.1928	45628	97.77 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.492→46.729 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21634	0	409	0	22043

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	22393
X-RAY DIFFRACTION	f_angle_d	1.301	30362
X-RAY DIFFRACTION	f_dihedral_angle_d	15.7	13550
X-RAY DIFFRACTION	f_chiral_restr	0.063	3500
X-RAY DIFFRACTION	f_plane_restr	0.008	3923

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 (%)
3.4922-3.5634	0.3257	125	0.2412	2267	X-RAY DIFFRACTION	89
3.5634-3.6409	0.3081	138	0.2238	2459	X-RAY DIFFRACTION	96
3.6409-3.7255	0.3173	122	0.2189	2461	X-RAY DIFFRACTION	96
3.7255-3.8187	0.2847	145	0.2157	2493	X-RAY DIFFRACTION	97
3.8187-3.9219	0.3001	118	0.2116	2482	X-RAY DIFFRACTION	97
3.9219-4.0372	0.2966	151	0.2114	2483	X-RAY DIFFRACTION	97
4.0372-4.1674	0.2988	137	0.1976	2514	X-RAY DIFFRACTION	98
4.1674-4.3163	0.2707	130	0.1774	2512	X-RAY DIFFRACTION	97
4.3163-4.489	0.2535	119	0.1693	2587	X-RAY DIFFRACTION	100
4.489-4.6931	0.2035	123	0.165	2553	X-RAY DIFFRACTION	99
4.6931-4.9402	0.2218	153	0.1704	2604	X-RAY DIFFRACTION	100
4.9402-5.2494	0.2307	122	0.1755	2596	X-RAY DIFFRACTION	100
5.2494-5.6541	0.2956	155	0.2011	2589	X-RAY DIFFRACTION	99
5.6541-6.2219	0.3044	142	0.1994	2605	X-RAY DIFFRACTION	99
6.2219-7.1195	0.2084	155	0.1892	2624	X-RAY DIFFRACTION	100
7.1195-8.9594	0.2191	139	0.1625	2691	X-RAY DIFFRACTION	100
8.9594-46.7331	0.241	143	0.174	2791	X-RAY DIFFRACTION	99

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	2.0358	0.394	0.7734	2.0054	-0.535	3.007	0.1137	-0.5452	-0.1206	0.8338	-0.1466	0.139	0.2376	-0.2851	0.0407	0.8047	-0.1561	0.0853	0.5165	0.06	0.5017	8.487	-24.2168	-6.2298
2	1.7344	0.4943	0.3585	1.7321	1.0088	2.4697	-0.0249	-0.0543	-0.3921	0.1173	-0.0482	-0.0664	0.2404	-0.0356	0.0843	0.6002	-0.113	-0.0354	0.3808	0.1377	0.4549	20.6701	-23.806	-22.5955
3	0.9729	0.6396	-0.4449	0.8033	0.5053	1.8347	-0.1323	0.0613	-0.0245	-0.0208	-0.0768	-0.0079	0.2709	-0.3963	0.1263	0.6466	0.038	-0.1375	0.3825	-0.0562	0.4394	18.8369	-23.3023	-34.6413
4	2.2729	-0.2064	0.1219	3.6178	1.6537	4.2167	-0.1671	0.623	0.3191	-0.2682	0.0733	0.0593	-0.4703	-0.2271	0.0712	0.5616	-0.0636	-0.0759	0.403	0.0373	0.3409	18.4371	-13.886	-33.605
5	1.4903	-0.3983	-1.0766	0.9086	0.0675	0.6921	0.012	0.0162	-0.0805	0.2024	-0.0116	0.2158	-0.0564	-0.3104	0.0436	0.6023	-0.1707	-0.0429	0.5774	0.0727	0.4242	8.0864	-14.5369	-15.2895
6	1.992	-0.377	0.2255	6.2484	-1.6088	5.7464	0.3361	-0.1925	-0.0512	1.3305	-0.1026	1.0941	-0.6908	-0.613	-0.071	0.6164	-0.0947	0.07	0.6994	-0.0089	0.5354	2.0352	-2.1087	-4.8411
7	0.5167	-0.5052	0.317	2.8056	0.5911	3.8769	-0.1563	0.1083	0.0893	-0.1487	-0.0603	-0.4081	0.0261	0.652	0.1381	0.3838	-0.0238	0.0236	0.5708	0.1451	0.6623	45.8248	-11.9025	-38.0036
8	1.5358	0.445	0.7661	2.2654	0.636	2.8756	-0.0498	-0.0302	0.0137	-0.0524	-0.1772	-0.639	-0.1492	0.1156	0.2155	0.5281	-0.1015	0.0533	0.4369	0.1635	0.322	31.9627	-10.0559	-23.4198
9	2.3167	-0.0461	-0.246	2.9915	0.4947	3.2594	0.158	-0.3147	-0.0437	0.2676	-0.2796	-0.6327	0.2555	0.2844	0.151	0.624	-0.0255	-0.1006	0.5276	0.138	0.3858	34.7727	-15.8421	-14.4245
10	2.1601	-0.2943	1.1913	3.828	-0.991	3.0346	0.1653	-0.4685	0.1697	0.2113	-0.2881	-0.2643	0.0757	0.4376	0.056	0.7148	-0.2023	-0.0084	0.5715	0.0798	0.3593	42.3213	-1.2339	-30.9589
11	7.5785	-3.3999	-2.4781	2.8143	2.294	4.1486	0.7915	1.249	1.1309	-0.2345	-0.7133	-0.7306	-1.125	-0.0862	-0.0782	0.6702	-0.1786	-0.0578	0.592	0.1669	0.5685	35.4366	10.4509	-37.4398
12	1.7691	-0.4915	-0.3972	1.5286	0.6283	2.479	0.1286	0.1491	0.1453	0.1946	-0.1082	0.2722	-0.8267	-0.4411	-0.0005	0.8694	0.1197	0.0406	0.4617	0.0894	0.5232	8.4823	22.8651	-55.137
13	3.9631	-0.3179	0.4196	2.2001	0.4893	3.3609	0.2138	0.7477	0.0579	-0.5674	-0.3043	0.2797	-0.7176	-0.354	0.0341	0.6698	0.1582	-0.0746	0.5487	0.033	0.4759	8.0043	14.6577	-73.8587
14	1.5191	-0.8268	0.4939	2.7927	-0.3694	1.2541	0.0256	-0.084	0.2596	0.4976	-0.039	-0.1433	-0.7877	0.0973	-0.0014	0.8097	-0.0214	0.0317	0.3686	0.0261	0.4389	24.2335	19.8516	-53.647
15	4.3163	1.3669	-1.8705	3.6292	-1.5343	3.3975	-0.362	0.8725	0.5497	-0.7329	0.308	0.6219	-0.2818	-0.6797	-0.1441	0.7317	0.1169	-0.1282	0.6795	0.0263	0.6185	4.3592	23.5198	6.1012
16	2.2732	1.1455	-1.2055	3.4933	-1.1935	3.2349	0.3889	0.3496	0.6646	-0.6334	-0.1256	0.2714	-0.1935	-0.0382	-0.0071	0.9978	-0.0208	0.0731	0.3962	0.0668	0.6687	17.5455	28.7929	5.5227
17	1.3757	0.2342	0.9378	1.627	0.0588	1.3673	-0.1724	-0.0252	0.2405	-0.1013	-0.1398	0.0104	-0.4323	-0.1155	0.2015	0.7197	0.0432	0.04	0.3766	0.0168	0.542	22.7284	21.3307	25.1842
18	3.3298	0.7999	0.2024	1.3253	0.3724	3.3754	-0.0263	-0.2737	0.0389	0.4386	0.0238	-0.0662	0.2923	-0.2231	0.0802	0.7052	-0.0135	0.0406	0.3527	-0.0392	0.4078	21.1109	11.9716	30.2176
19	2.4663	0.8997	-1.6556	0.491	-0.5142	1.1409	-0.1035	0.5599	0.3904	-0.2604	-0.1495	0.1513	-0.2988	-1.1506	-0.0173	1.0105	0.0887	-0.0331	0.5722	0.051	0.4143	13.3088	16.136	11.9235
20	3.915	1.2147	-0.0255	6.0318	0.9094	8.1075	-0.1713	0.2313	0.8076	-0.0443	-0.0802	-0.2622	-0.1477	-0.9643	0.3929	0.5707	0.1417	-0.0116	0.5761	0.0258	0.4887	3.489	19.0617	17.6823
21	5.6036	-1.3735	-0.083	2.7187	1.2067	1.4882	-0.0735	0.0812	0.391	1.0818	-0.9332	1.2217	-0.0327	-0.8353	0.5043	0.7573	0.0028	0.0949	0.8156	-0.0044	0.4955	-2.6035	10.2759	17.7255
22	7.5655	-3.4531	-2.9482	5.9249	1.3852	3.225	0.4814	-0.2748	-0.1541	-1.4429	-0.1227	0.5687	-0.832	0.055	-0.3736	0.8467	-0.0582	0.055	0.5487	-0.0265	0.5154	3.3304	2.6713	7.421
23	2.3206	0.0325	0.0103	1.3287	0.3751	3.222	-0.2389	-0.1481	0.5734	0.475	0.0636	-0.261	-0.6974	-0.0574	0.0539	0.7201	0.0689	-0.0317	0.4059	0.0373	0.6344	51.5438	-34.8067	-48.6572
24	0.9313	-0.9293	0.2521	1.6053	-0.1884	1.9535	0.2259	0.4184	0.2575	0.2388	-0.0778	0.116	-0.3482	-0.3809	0.0155	0.5632	0.098	0.0682	0.4113	0.0162	0.482	45.4063	-50.0385	-58.7924
25	1.8986	0.2447	0.3803	1.7122	0.0766	1.8671	0.0326	0.2123	0.1773	-0.2246	-0.1235	0.1723	-0.282	0.0101	0.0193	0.548	0.145	0.0459	0.5292	0.0574	0.4203	46.4175	-49.9074	-68.741
26	4.5727	-3.8619	0.2926	4.9253	0.9796	0.9109	-0.0262	0.4178	0.2393	0.0121	0.0295	-0.3149	-0.242	0.0087	-0.083	0.5805	-0.0346	0.0455	0.4388	0.0914	0.401	67.0784	-43.2971	-55.2011
27	1.4747	0.1441	-0.323	2.3928	1.8363	3.7783	-0.4345	-0.1887	-0.017	1.1538	0.363	-0.9779	0.5778	0.5665	0.1577	0.7076	-0.0347	-0.0776	0.5298	0.1041	0.8134	52.1167	-1.0604	40.0669
28	1.218	0.41	0.2253	1.2841	0.2742	1.8805	-0.0292	0.1535	-0.0297	0.0556	-0.0853	-0.2879	-0.0179	0.2457	0.0882	0.6184	-0.0149	0.0337	0.4174	0.0655	0.5293	39.5052	9.95	24.4138
29	4.2548	0.6122	-1.0984	2.7977	-0.1227	2.2012	-0.2891	-0.207	-0.1359	-0.0835	-0.1637	-0.393	0.3422	0.4687	0.5055	0.6266	0.0751	0.0561	0.4322	-0.0226	0.5038	41.6136	-11.7699	32.9968
30	1.7707	-0.3231	0.3246	0.5424	0.1766	1.8797	0.0923	0.4149	-0.2123	-0.0604	-0.1193	0.2204	0.484	-0.5407	-0.1091	0.6632	-0.0585	-0.1101	0.8084	-0.0765	0.8187	34.0089	-78.1761	-79.7937
31	1.7078	0.2853	0.0839	1.3883	0.0695	1.7033	0.0172	0.5796	0.0327	0.2365	-0.1038	0.2335	0.0607	-0.0455	-0.3056	0.6271	0.089	0.0149	0.5081	-0.0326	0.4966	44.9931	-67.6246	-66.4793
32	1.8999	0.343	-0.1694	1.7126	0.7266	1.8487	0.0373	0.0589	-0.0574	0.147	-0.0632	0.2461	0.279	-0.3929	-0.3813	0.6157	-0.0038	0.0241	0.4995	0.0514	0.5042	39.3469	-65.8897	-57.1153
33	1.4354	-0.2025	-0.2845	1.8711	0.6973	1.1133	0.032	0.0173	-0.4555	0.0356	-0.2606	0.2506	0.0098	-0.584	-0.2415	0.6498	0.02	-0.1193	0.6694	-0.0566	0.5748	45.1077	-81.6141	-73.3886
34	8.2975	1.267	-0.1275	0.5481	0.4411	1.9196	-0.0952	0.6181	-1.0097	-0.5951	0.2715	-0.5612	0.7055	-0.1457	-0.1075	0.7495	0.0227	-0.0657	0.6194	-0.0254	0.5664	58.0339	-83.6134	-80.7994
35	1.1199	0.4253	0.1053	1.8623	0.6397	2.4863	-0.2311	0.5701	0.0399	-0.3181	-0.2949	0.7014	0.1774	-1.3504	0.357	0.65	-0.1672	-0.1026	1.3075	-0.1623	0.7633	-5.5141	-7.9507	-79.0153
36	2.3922	0.1995	-0.583	3.8387	0.4423	2.721	0.0042	0.2204	0.0385	0.3517	-0.2887	0.9992	0.2548	-0.8194	0.1611	0.4226	-0.0118	0.0439	0.7301	-0.0484	0.7258	-5.1781	2.6733	-58.6193
37	2.8635	-0.3226	-1.2782	4.5013	0.8328	3.7682	-0.0301	-0.1427	-0.0602	0.521	-0.1819	0.4062	-0.3383	-0.4359	0.2425	0.645	0.0136	0.0252	0.4451	-0.0309	0.403	6.1637	0.9943	-58.6404
38	0.5179	-0.6387	0.83	2.2933	-0.2594	1.7334	-0.0862	0.3824	0.274	-0.0859	0.0137	0.7036	0.7328	-1.302	0.455	0.5218	-0.3463	-0.1142	1.0077	-0.1126	0.6097	1.9927	-7.2591	-75.924
39	7.6393	-1.3927	-1.5394	0.8059	0.1612	1.083	-0.4543	0.0227	-0.3661	0.0541	-0.0541	0.3314	0.793	-0.4474	0.3783	0.7955	-0.3158	0.0196	0.653	-0.1163	0.5917	8.6942	-18.6901	-76.3683

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 41 through 157 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 158 through 222 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 223 through 252 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 253 through 272 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 273 through 368 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 369 through 400 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 41 through 149 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 150 through 191 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 192 through 298 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 299 through 368 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 369 through 399 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 41 through 222 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 223 through 298 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 299 through 399 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 42 through 90 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 91 through 123 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 124 through 252 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 253 through 298 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 299 through 335 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 336 through 352 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 353 through 368 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 369 through 399 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 41 through 116 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 117 through 192 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 193 through 335 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 336 through 399 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 41 through 91 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 92 through 335 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 336 through 399 )
30	X-RAY DIFFRACTION	30	chain 'G' and (resid 41 through 149 )
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 150 through 191 )
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 192 through 298 )
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 299 through 368 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 369 through 399 )
35	X-RAY DIFFRACTION	35	chain 'H' and (resid 44 through 161 )
36	X-RAY DIFFRACTION	36	chain 'H' and (resid 162 through 256 )
37	X-RAY DIFFRACTION	37	chain 'H' and (resid 257 through 296 )
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 297 through 335 )
39	X-RAY DIFFRACTION	39	chain 'H' and (resid 336 through 398 )

-
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