PDB-4xgi: Crystal structure of Glutamate dehydrogenase from Burkholderia th...

ID or keywords:

Entry

Database: PDB / ID: 4xgi

Title

Crystal structure of Glutamate dehydrogenase from Burkholderia thailandensis

Components

Glutamate dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID /

Glutamate dehydrogenase /

Burkholderia thailandensis /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / amino acid metabolic process /

nucleotide binding
Similarity search - Function

Biological species

Burkholderia thailandensis (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of Glutamate dehydrogenase from Burkholderia thailandensis
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Dec 30, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Source and taxonomy Category: entity_src_gen / pdbx_struct_oper_list ...entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / software Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Sep 27, 2023	Group: 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 / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4xgi.cif.gz	976.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4xgi.ent.gz	811.6 KB	Display	PDB format
PDBx/mmJSON format	4xgi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xg/4xgi ftp://data.pdbj.org/pub/pdb/validation_reports/xg/4xgi	HTTPS FTP

-
Related structure data

Related structure data	3aoeS S: Starting model for refinement
Similar structure data	5a02-d 5ijz-2 4ndz-2 3hnp-d 2vhx-d 3vjc-d 5xw0-1 5a03-d 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	TargetTrack: SSGCID-ButhA.17991.a

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1)

Deposited unit

A: Glutamate dehydrogenase

B: Glutamate dehydrogenase

C: Glutamate dehydrogenase

D: Glutamate dehydrogenase

E: Glutamate dehydrogenase

F: Glutamate dehydrogenase

hetero molecules

288 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)	95.490, 93.520, 158.370
Angle α, β, γ (deg.)	90.000, 106.230, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

biological unit is a hexamer, same as the asymmetric unit

#1: Protein	Glutamate dehydrogenase / Mass: 47061.262 Da / Num. of mol.: 6 / Fragment: ButhA.17991.a.A1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301) (bacteria) Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I1224, DR63_1118 / Plasmid: ButhA.17991.a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2SZ78
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid Mass: 146.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₅H₆O₅
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1641 / 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: 2.3 Å³/Da / Density % sol: 46.51 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Microlytics MCSG1 screen F1: 20% PEG 5000MME, 100mM BisTris pH 6.5; ButhA.17991.a.A1.PW33475 at 20mg/ml with 2.5mM NAD and 2.5mM Glu; cryo: 20% EG; tray 257704f1, puck smx9-3

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 18, 2014

Radiation

Monochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 174736 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / B_iso Wilson estimate: 22.28 Å² / R_merge F obs: 0.997 / R_merge(I) obs: 0.083 / R_rim(I) all: 0.09 / Χ²: 0.968 / Net I/σ(I): 14.91 / Num. measured all: 1153986

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	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
2-2.05	4.6	0.895	0.392	3.3	56757	13267	12288	0.443	92.6
2.05-2.11		0.924	0.328	4.21	61880	12998	12364	0.367	95.1
2.11-2.17		0.944	0.289	5.11	66282	12653	12218	0.321	96.6
2.17-2.24		0.946	0.337	5.12	65171	12241	11512	0.372	94
2.24-2.31		0.97	0.211	9.2	62220	11866	10937	0.233	92.2
2.31-2.39		0.976	0.213	8.28	75778	11565	11202	0.231	96.9
2.39-2.48		0.985	0.171	10.82	80468	11020	10752	0.183	97.6
2.48-2.58		0.987	0.148	12.19	78014	10715	10452	0.16	97.5
2.58-2.7		0.99	0.128	13.94	74851	10214	10009	0.138	98
2.7-2.83		0.992	0.11	16.12	71707	9838	9649	0.118	98.1
2.83-2.98		0.994	0.096	17.88	68221	9338	9196	0.103	98.5
2.98-3.16		0.995	0.084	20.05	64193	8812	8673	0.09	98.4
3.16-3.38		0.996	0.073	23.07	60197	8306	8200	0.079	98.7
3.38-3.65		0.996	0.066	25.74	55051	7729	7619	0.072	98.6
3.65-4		0.996	0.062	28.72	49355	7140	7032	0.067	98.5
4-4.47		0.997	0.053	31.25	45662	6488	6401	0.057	98.7
4.47-5.16		0.997	0.05	32.64	40615	5724	5643	0.054	98.6
5.16-6.32		0.997	0.049	30.99	35177	4834	4785	0.053	99
6.32-8.94		0.999	0.041	33.55	27629	3789	3743	0.044	98.8
8.94-50		0.995	0.038	36.44	14758	2132	2061	0.041	96.7

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2 Å	45.84 Å
Translation	2 Å	45.84 Å

-
Processing

Software

Name	Classification
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3aoe, search with two domains

3aoe

Resolution: 2→45.842 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2222	1995	1.14 %	Random selection
R_work	0.1761	172728	-	-
obs	0.1766	174723	96.75 %	-

Solvent computation

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

Displacement parameters

B_iso max: 89.69 Å² / B_iso mean: 30.5192 Å² / B_iso min: 9.6 Å²

Refinement step

Cycle: final / Resolution: 2→45.842 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18661	0	348	1643	20652
B_iso mean	-	-	26.41	35.04	-
Num. residues	-	-	-	-	2492

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	19523
X-RAY DIFFRACTION	f_angle_d	1.033	26605
X-RAY DIFFRACTION	f_chiral_restr	0.039	3026
X-RAY DIFFRACTION	f_plane_restr	0.005	3463
X-RAY DIFFRACTION	f_dihedral_angle_d	13.899	7034

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2-2.05	0.2402	130	0.1864	11711	11841	93
2.05-2.1055	0.2598	150	0.199	12090	12240	95
2.1055-2.1674	0.2658	137	0.2091	12281	12418	97
2.1674-2.2374	0.3204	132	0.2585	11953	12085	94
2.2374-2.3173	0.4281	138	0.322	11703	11841	92
2.3173-2.4101	0.2409	147	0.2077	12356	12503	97
2.4101-2.5198	0.2541	139	0.186	12457	12596	98
2.5198-2.6526	0.2609	141	0.1826	12423	12564	98
2.6526-2.8188	0.2238	151	0.1715	12473	12624	98
2.8188-3.0364	0.2447	143	0.1774	12570	12713	98
3.0364-3.3419	0.2112	142	0.1694	12592	12734	99
3.3419-3.8252	0.2062	149	0.1555	12610	12759	99
3.8252-4.8186	0.1616	147	0.1305	12654	12801	99
4.8186-45.8545	0.1597	149	0.147	12855	13004	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	1.7392	0.8084	-1.1982	1.2342	-1.4458	3.5727	-0.098	0.17	0.2554	-0.1749	-0.0087	-0.0216	-0.108	0.0516	0.1108	0.2258	-0.0006	-0.0168	0.1105	0.0316	0.2463	42.8288	33.9995	108.7133
2	0.9535	0.404	-0.2044	0.5917	-0.3319	1.6097	-0.0397	-0.0232	0.1637	0.0888	0.0365	-0.1727	-0.1324	0.0607	-0.0107	0.1527	0.0042	-0.0093	0.0846	-0.0101	0.2143	45.6665	28.1683	121.5791
3	1.6921	0.1445	-0.5697	1.388	-0.6977	1.7154	-0.0404	-0.0653	0.0484	0.017	0.0372	-0.1537	-0.017	0.0655	0.0244	0.1219	0.0185	-0.0031	0.086	-0.0243	0.1712	44.462	20.1562	127.261
4	1.4879	0.8286	-0.7381	1.2318	-0.9537	1.2571	-0.0326	-0.0785	-0.0217	0.0674	-0.1075	-0.6143	0.0635	0.2596	0.1793	0.1178	0.0109	-0.0143	0.1478	0.0189	0.3827	57.8022	20.2045	125.5271
5	1.4692	0.735	0.0899	1.3966	0.5832	0.9719	-0.053	-0.1032	0.198	0.2791	-0.1091	-0.7106	-0.3102	0.1173	0.0356	0.2748	-0.1007	-0.1901	0.1353	0.0656	0.6536	63.6777	43.8557	126.8834
6	1.0278	-0.3387	0.2618	0.2041	0.0569	1.993	0.1811	-0.1186	-0.1084	0.1226	-0.2792	-0.3926	0.2859	0.252	0.0303	0.1972	-0.0214	-0.0364	0.2365	0.0778	0.4363	62.2154	27.6189	116.1298
7	0.8697	0.6472	0.5835	1.2826	0.6566	1.565	-0.0377	0.2433	0.014	-0.1843	0.0812	-0.5903	-0.0223	0.4426	-0.0498	0.1649	-0.0151	0.0672	0.2674	0.0522	0.4761	61.3637	28.5649	105.5443
8	4.0751	-0.4547	0.5843	0.1167	0.2114	1.5094	-0.1916	-0.571	-0.3485	0.0346	-0.0075	-0.0279	-0.1171	-0.0949	0.1888	0.1971	0.0305	-0.0151	0.246	0.0536	0.1589	54.8977	-7.4664	148.6244
9	1.4901	1.4923	1.0345	7.6313	3.2235	2.6331	-0.1767	-0.1041	0.2463	-0.0377	-0.0659	0.2993	-0.1288	0.0879	0.1752	0.098	0.0027	0.0109	0.1466	0.0339	0.0838	48.5542	-4.4253	138.2767
10	1.5941	0.4731	0.5867	1.5106	0.836	0.8864	0.0001	-0.0695	0.0328	-0.1114	-0.0857	-0.0371	0.1393	0.0566	0.0767	0.1658	0.0152	0.0024	0.1271	0.0492	0.1132	53.6812	-13.4016	131.8662
11	1.8475	0.1848	0.754	0.9332	0.3011	1.8569	0.0185	0.0896	-0.0001	-0.0858	-0.1318	-0.0706	0.0535	0.161	0.1082	0.183	0.0059	0.018	0.1256	0.0453	0.1192	51.176	-14.8506	120.2943
12	1.7606	0.2391	0.7645	0.5179	0.1905	1.2821	-0.0758	0.5435	0.4176	-0.1308	-0.1939	-0.1805	-0.0081	0.6749	0.0698	0.1907	-0.0237	0.0333	0.328	0.1082	0.2454	69.1085	-8.9586	123.4187
13	1.7959	-0.3976	0.1477	1.8866	0.2112	1.4725	-0.0196	-0.0801	-0.2289	0.003	-0.0828	-0.3056	0.1533	0.4092	0.0605	0.1351	0.0486	0.0289	0.3006	0.1205	0.2553	76.0903	-21.5361	137.8827
14	0.5332	0.5432	0.7551	1.248	-0.0316	6.6364	0.0332	0.2599	-0.1119	-0.188	0.1093	0.0896	-0.5044	0.3221	-0.0199	0.1743	-0.0119	-0.0003	0.2628	0.0364	0.2773	68.5818	-5.1331	130.2985
15	2.5146	0.2922	2.1238	3.2811	2.1772	4.0782	-0.1472	0.2872	0.4371	-0.8647	-0.1293	-0.5038	-1.0255	1.0782	0.1456	0.3755	-0.0823	0.0455	0.3424	0.1745	0.4315	76.0587	0.5144	131.999
16	1.8311	-1.6103	0.172	1.8909	-0.4951	0.9702	-0.148	-0.1834	0.5073	0.2174	-0.0614	-0.457	-0.1336	0.0628	0.171	0.152	-0.0489	-0.0474	0.1609	0.017	0.224	59.5452	6.2039	141.1663
17	7.4509	3.0244	-0.3056	2.4384	-0.0432	0.0241	-0.0255	-0.5348	-0.3854	0.0095	-0.037	-0.1867	0.3059	-0.0535	0.0175	0.2485	-0.0508	0.0321	0.242	0.0956	0.1984	32.8385	-24.5055	142.1121
18	0.9562	0.6265	0.1356	1.8707	0.7903	1.7127	0.0025	-0.0419	-0.042	0.0665	0.038	-0.032	0.0799	-0.1801	-0.0343	0.1192	-0.0063	0.0062	0.1675	0.0471	0.0931	32.0993	-9.6258	137.9424
19	1.7275	0.6197	0.3594	2.4893	-1.0777	1.5173	0.0166	-0.0344	0.0612	-0.0409	0.0819	0.0652	-0.0399	-0.1858	-0.086	0.0934	-0	0.0144	0.1741	0.0011	0.101	30.4916	4.1717	135.4484
20	2.495	2.1209	-1.025	2.5559	-0.8948	0.8731	-0.1018	-0.0253	0.2682	-0.2078	0.3291	0.5939	0.1096	-0.5678	-0.2209	0.1312	-0.0521	-0.0224	0.449	0.1157	0.2694	13.1777	-4.0165	136.1826
21	1.5137	0.1161	-0.7151	0.9615	-0.3151	1.4644	-0.0223	-0.2632	0.1136	0.1013	0.2152	0.267	-0.0008	-0.4857	-0.1059	0.0738	-0.0321	0.1184	0.5882	0.1452	0.2171	11.9797	-11.7096	155.2005
22	1.3848	-0.002	-0.1771	1.1421	0.9555	0.8193	0.1171	0.0683	0.2835	-0.2565	0.1147	0.3888	-0.0574	-0.3949	-0.1945	0.1879	-0.0603	0.021	0.3777	0.0762	0.2904	14.5742	-11.7167	135.6693
23	1.3283	-1.549	-0.7977	3.0574	0.7479	1.5021	-0.0084	0.3177	-0.2238	-0.4761	0.106	0.6185	0.1172	-0.7883	-0.1453	0.2886	-0.2734	-0.0641	0.6728	0.0959	0.3467	7.28	-17.4201	133.4158
24	2.4926	0.9462	-1.8083	0.8027	-0.6909	2.6281	-0.1479	0.0145	-0.0363	-0.1427	0.0818	0.189	0.5446	-0.3698	0.1218	0.2667	-0.1109	-0.0096	0.2097	0.0115	0.1997	24.4242	-25.1258	128.1743
25	8.0287	-0.2132	0.6047	0.89	-0.4116	1.6433	-0.0381	0.7287	-0.1877	-0.2038	-0.0675	0.0219	-0.0273	0.0974	0.1077	0.2771	-0.0023	-0.0224	0.174	-0.0012	0.1015	26.2314	-9.9554	80.9724
26	6.094	-5.0171	3.4656	6.0261	-3.0292	3.4192	0.094	0.1704	0.2592	-0.3499	-0.2013	-0.0688	0.0497	-0.0325	0.1919	0.2164	-0.0033	0.0052	0.12	-0.0003	0.1054	30.8471	-5.0671	91.0903
27	1.2028	-0.1852	0.3579	0.9187	-0.4925	0.3328	0.0082	0.0179	-0.0338	-0.0466	-0.0359	0.0345	0.1722	-0.0183	0.0286	0.2985	-0.0013	-0.006	0.145	-0.0349	0.0883	29.6817	-16.4057	97.2359
28	2.0215	-0.0763	0.6964	1.2703	-0.4556	1.523	0.0541	-0.1295	-0.0413	0.0366	-0.1006	-0.0174	0.1264	-0.1031	0.0564	0.224	-0.0219	-0.0035	0.1299	-0.0179	0.0903	32.7148	-17.5905	108.7016
29	1.0987	0.2905	0.1441	1.0714	0.0437	0.8029	-0.0719	-0.5564	0.086	0.1737	-0.2051	0.2102	0.0641	-0.6897	0.2435	0.2646	-0.0432	0.0376	0.3319	-0.0724	0.1735	14.1705	-17.5846	106.66
30	2.0224	0.2692	0.4402	2.3259	0.5458	1.2108	0.085	-0.1123	-0.1978	0.0706	-0.1427	0.1702	0.2655	-0.2341	0.0628	0.3166	-0.1036	-0.0028	0.2004	-0.0428	0.1572	11.0102	-30.9308	90.5502
31	1.8131	-0.3196	-0.2901	1.8356	-0.6192	0.3304	-0.1284	-0.2462	0.038	0.3956	-0.0646	0.1067	-0.2461	-0.0522	0.1974	0.3426	-0.0276	-0.0388	0.223	-0.0358	0.1903	12.7103	-13.585	99.2431
32	2.185	-0.6898	1.2093	4.3919	-3.8829	3.8301	-0.0464	-0.4651	0.3201	0.7059	0.0506	0.6798	-1.1328	-0.7992	-0.0154	0.3172	0.0188	0.0213	0.386	-0.1973	0.4152	3.916	-10.6417	98.0771
33	3.8725	3.5455	1.8935	4.9064	2.0133	1.5546	-0.174	0.1799	0.2225	-0.3215	0.0334	0.4396	-0.08	-0.0245	0.1923	0.1931	0.0246	-0.0199	0.145	-0.0086	0.1684	17.7127	0.9494	89.6165
34	6.6112	0.1459	-1.8245	0.4768	0.35	1.5254	0.0082	-0.2861	0.9877	0.162	0.1452	0.1246	-0.1226	0.0934	-0.2188	0.1885	0.0452	0.0056	0.1802	-0.0692	0.2697	21.1008	35.1859	124.7875
35	1.2094	0.1815	-0.3118	0.9379	-0.6992	2.2032	-0.027	-0.063	0.1259	-0.0268	0.0516	0.0706	-0.153	-0.1586	-0.0319	0.1398	0.0348	0.0119	0.0951	-0.0059	0.1616	24.4877	24.7745	113.9023
36	1.3665	-0.5254	-0.5039	0.894	0.4336	1.2508	-0.0026	0.0666	-0.1385	-0.0293	0.0006	0.1806	0.1225	-0.1454	0.0215	0.1631	-0.0095	-0.0083	0.1156	0.0166	0.1765	19.2242	15.3093	105.3955
37	2.4709	-0.4101	0.1179	1.1947	-0.1584	1.0691	0.0185	0.5439	0.1269	-0.3126	0.054	0.5111	0.1364	-0.3996	-0.0095	0.1481	0.0643	-0.024	0.4424	0.08	0.3849	-2.6134	29.4911	103.4194
38	2.1979	-0.8963	0.5139	2.2981	-0.1671	1.2538	0.1734	0.7467	0.3925	-0.2334	-0.1594	0.1156	-0.1347	-0.2305	-0.0106	0.1865	0.0893	0.0037	0.4847	0.1236	0.3596	0.9992	34.4496	99.3902
39	2.5745	-0.702	-0.0564	1.8538	0.4076	1.9775	-0.0838	-0.1578	0.4294	0.0159	0.0756	0.1761	-0.2823	-0.1796	0.0015	0.1785	0.0756	0.0277	0.2649	0.0187	0.3347	5.3673	37.7171	116.1984
40	1.284	-1.2056	-0.9095	5.7852	2.0225	2.283	0.2001	0.2435	-0.2078	-0.1658	-0.1552	-0.0008	0.1486	-0.3209	-0.0147	0.1665	0.012	0.0043	0.3003	0.0051	0.2813	7.9463	18.1105	115.5476
41	1.4417	-1.6959	-0.934	2.4901	0.5359	4.9929	-0.0251	-0.2229	-0.3783	0.0304	0.0543	0.7666	0.6344	-0.8963	-0.0181	0.2274	-0.0397	0.0283	0.3859	0.0884	0.3735	0.4752	16.9374	122.4046
42	2.0489	-0.9108	0.1046	1.4532	-0.3842	0.8463	-0.1239	-0.2745	0.116	0.1649	0.1602	0.0715	0.017	-0.289	-0.0269	0.1575	0.0328	0.0471	0.2467	-0.0026	0.16	16.4152	21.2114	131.7825
43	6.0704	-0.4357	-0.8092	1.7267	0.2543	1.112	0.0259	0.611	-0.2497	-0.1464	-0.1037	0.0202	0.2902	0.0975	0.0917	0.391	0.082	0.0497	0.2091	-0.0248	0.1721	52.9955	-18.9971	86.5342
44	5.4779	-4.1964	1.9734	4.49	-2.4195	2.0553	-0.0544	-0.1208	-0.2332	0.1408	-0.001	0.0436	0.2248	0.1477	0.0001	0.2626	0.0396	0.0042	0.1453	-0.0006	0.1044	47.8785	-13.3873	96.0022
45	1.4704	-0.5464	0.1554	1.4631	-0.5809	0.5033	0.0581	0.137	0.0522	-0.2781	-0.1239	-0.1296	0.0625	0.1347	0.071	0.2377	0.0279	0.0271	0.1641	0.0316	0.1036	49.0706	-1.913	90.0379
46	2.5528	-1.1833	-0.0279	2.3222	0.2398	1.7516	-0.0245	-0.0808	0.1644	-0.1059	-0.0246	-0.0315	-0.022	0.1996	0.0629	0.1678	-0.0026	0.0077	0.1263	0.0179	0.1111	45.5485	8.1774	95.2282
47	1.9959	-1.3186	0.0628	1.7942	0.1826	0.3302	0.0631	-0.1376	0.4434	-0.0548	-0.0019	-0.4864	-0.0163	0.504	-0.0841	0.204	0.0203	0.03	0.3695	0.0613	0.3073	64.4678	6.4821	94.496
48	1.9045	0.0919	-0.5531	0.8824	0.2077	1.6935	-0.0698	0.5214	0.3708	-0.3499	-0.1179	-0.4402	-0.0487	0.4697	0.1097	0.3198	0.0332	0.1144	0.5288	0.1947	0.3941	69.2792	5.8981	74.1233
49	1.1852	-0.1798	-0.3038	2.3759	-0.1137	0.6587	-0.0363	0.2115	0.0098	-0.1667	-0.1276	-0.2371	0.3046	0.4559	0.0468	0.2791	0.1357	0.0958	0.3881	0.0809	0.2879	65.7332	-7.0668	83.7068
50	1.0984	-2.0018	-0.6746	6.2432	0.2084	1.5397	-0.0638	-0.2529	0.0539	0.5987	-0.0016	-0.8442	-0.0485	0.7373	-0.1452	0.2501	0.0918	-0.0172	0.6892	0.0918	0.3803	74.5946	-4.0125	96.3065
51	1.2686	0.5596	-0.6882	0.8971	-0.2141	1.618	0.0091	-0.0803	-0.1432	-0.0869	-0.1273	-0.316	0.319	0.4663	0.1576	0.2397	0.0997	0.0454	0.2704	0.0682	0.2176	61.2434	-17.8083	100.4949

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 64 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 65 through 135 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 136 through 168 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 169 through 222 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 223 through 348 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 349 through 381 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 382 through 434 )	A
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 13 through 39 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 40 through 64 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 65 through 135 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 136 through 183 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 184 through 223 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 224 through 348 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 349 through 381 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 382 through 407 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 408 through 434 )	B
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 13 through 39 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 40 through 135 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 136 through 183 )	C
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 184 through 223 )	C
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 224 through 348 )	C
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 349 through 381 )	C
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 382 through 407 )	C
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 408 through 434 )	C
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 13 through 39 )	D
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 40 through 64 )	D
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 65 through 135 )	D
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 136 through 183 )	D
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 184 through 222 )	D
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 223 through 348 )	D
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 349 through 381 )	D
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 382 through 407 )	D
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 408 through 434 )	D
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 13 through 39 )	E
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 40 through 135 )	E
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 136 through 223 )	E
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 224 through 272 )	E
38	X-RAY DIFFRACTION	38	chain 'E' and (resid 273 through 310 )	E
39	X-RAY DIFFRACTION	39	chain 'E' and (resid 311 through 348 )	E
40	X-RAY DIFFRACTION	40	chain 'E' and (resid 349 through 382 )	E
41	X-RAY DIFFRACTION	41	chain 'E' and (resid 383 through 407 )	E
42	X-RAY DIFFRACTION	42	chain 'E' and (resid 408 through 434 )	E
43	X-RAY DIFFRACTION	43	chain 'F' and (resid 13 through 39 )	F
44	X-RAY DIFFRACTION	44	chain 'F' and (resid 40 through 64 )	F
45	X-RAY DIFFRACTION	45	chain 'F' and (resid 65 through 135 )	F
46	X-RAY DIFFRACTION	46	chain 'F' and (resid 136 through 183 )	F
47	X-RAY DIFFRACTION	47	chain 'F' and (resid 184 through 223 )	F
48	X-RAY DIFFRACTION	48	chain 'F' and (resid 224 through 310 )	F
49	X-RAY DIFFRACTION	49	chain 'F' and (resid 311 through 381 )	F
50	X-RAY DIFFRACTION	50	chain 'F' and (resid 382 through 407 )	F
51	X-RAY DIFFRACTION	51	chain 'F' and (resid 408 through 434 )	F

-
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