PDB-6mgj: Crystal structure of the catalytic domain from GH74 enzyme PoGH74...

ID or keywords:

Entry

Database: PDB / ID: 6mgj

Title

Crystal structure of the catalytic domain from GH74 enzyme PoGH74 from Paenibacillus odorifer, apoenzyme

Components

Xyloglucanase

Keywords

HYDROLASE / GLYCOSYLHYDROLASE / FAMILY GH74 / XYLOGLUCANASE

Function / homology

Function and homology information

xyloglucan metabolic process / hydrolase activity, acting on glycosyl bonds / cellulose binding / polysaccharide catabolic process / metal ion binding
Similarity search - Function

Biological species

Paenibacillus odorifer (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Stogios, P.J. / Skarina, T. / Nocek, B. / Arnal, G. / Brumer, H. / Savchenko, A.

Funding support

Canada, 1items

Citation

Journal: Biochem. J. / Year: 2018
Title: Structural enzymology reveals the molecular basis of substrate regiospecificity and processivity of an exemplar bacterial glycoside hydrolase family 74endo-xyloglucanase.
Authors: Arnal, G. / Stogios, P.J. / Asohan, J. / Skarina, T. / Savchenko, A. / Brumer, H.

History

Deposition	Sep 14, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 23, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 11, 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 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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
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	6mgj.cif.gz	2.4 MB	Display	PDBx/mmCIF format
PDB format	pdb6mgj.ent.gz	2 MB	Display	PDB format
PDBx/mmJSON format	6mgj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6mgj_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	6mgj_full_validation.pdf.gz	2.8 MB	Display
Data in XML	6mgj_validation.xml.gz	296.5 KB	Display
Data in CIF	6mgj_validation.cif.gz	468 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mg/6mgj ftp://data.pdbj.org/pub/pdb/validation_reports/mg/6mgj	HTTPS FTP

-
Related structure data

Related structure data	6mgkC 6mglC 2cn3S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6mgk-3 6mgk-2 5fkt-2 6mgk-1 4lgn-d 5jwz-2 5fkr-d 2pwz-1 3lk6-3 4k7g-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) 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) 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

6mgkC

6mglC

2cn3S

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	#141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Xyloglucanase

B: Xyloglucanase

C: Xyloglucanase

D: Xyloglucanase

E: Xyloglucanase

F: Xyloglucanase

G: Xyloglucanase

H: Xyloglucanase

hetero molecules

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

1

A: Xyloglucanase

hetero molecules

defined by author&software
83.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Xyloglucanase

hetero molecules

defined by author&software
81.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Xyloglucanase

hetero molecules

defined by author&software
81.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Xyloglucanase

hetero molecules

defined by author&software
82.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Xyloglucanase

hetero molecules

defined by author&software
82.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Xyloglucanase

hetero molecules

defined by author&software
83.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

G: Xyloglucanase

hetero molecules

defined by author&software
82.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

H: Xyloglucanase

hetero molecules

defined by author&software
82.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	239.094, 226.674, 187.224
Angle α, β, γ (deg.)	90.00, 114.07, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-1438- HOH
2	1	C-1855- HOH
3	1	F-1246- HOH
4	1	F-1514- HOH
5	1	F-2044- HOH
6	1	G-1566- HOH
7	1	G-1922- HOH

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	Xyloglucanase Mass: 81027.398 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus odorifer (bacteria) / Gene: BSK60_29080 / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1R0YRH0

-
Non-polymers , 6 types, 9698 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Formula: Mg
#3: Chemical	ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL Mass: 634.751 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Formula: C₂₈H₅₈O₁₅
#4: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 9639 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Sequence details	The sequence of xyloglucanase is from GenBank: AIQ73809

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.57 Å³/Da / Density % sol: 65.58 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.1 M Bis-Tris pH 6.9, 0.2 M sodium acetate, 25% PEG 8000, 0.1 M glucose, 10 mM xylose

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 2→40 Å / Num. obs: 613090 / % possible obs: 99.7 % / Redundancy: 5.4 % / R_merge(I) obs: 0.125 / R_pim(I) all: 0.056 / Net I/σ(I): 12.33
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.704 / Num. unique obs: 30562 / CC_1/2: 0.758 / R_pim(I) all: 0.315 / % possible all: 99.7

-
Processing

Software

Name	Version	Classification
PHENIX	(dev_3092: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2CN3

2cn3

Resolution: 2→39.776 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1765	3538	0.33 %	RANDOM
R_work	0.1489	-	-	-
obs	0.149	601755	87.96 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→39.776 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	45280	0	412	9639	55331

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	47054
X-RAY DIFFRACTION	f_angle_d	0.741	64232
X-RAY DIFFRACTION	f_dihedral_angle_d	13.002	16286
X-RAY DIFFRACTION	f_chiral_restr	0.051	6855
X-RAY DIFFRACTION	f_plane_restr	0.004	8267

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 (%)
2-2.0274	0.2698	89	0.2227	26452	X-RAY DIFFRACTION	55
2.0274-2.0564	0.2545	92	0.2122	28582	X-RAY DIFFRACTION	59
2.0564-2.0871	0.2226	100	0.2085	30093	X-RAY DIFFRACTION	62
2.0871-2.1197	0.2134	106	0.2027	32047	X-RAY DIFFRACTION	66
2.1197-2.1544	0.2367	116	0.1969	34009	X-RAY DIFFRACTION	70
2.1544-2.1916	0.2035	120	0.1921	36057	X-RAY DIFFRACTION	75
2.1916-2.2314	0.2194	127	0.1908	38138	X-RAY DIFFRACTION	79
2.2314-2.2743	0.2168	135	0.1903	39846	X-RAY DIFFRACTION	83
2.2743-2.3207	0.2063	143	0.1861	41345	X-RAY DIFFRACTION	85
2.3207-2.3712	0.2304	142	0.1843	42999	X-RAY DIFFRACTION	89
2.3712-2.4263	0.2093	154	0.1813	45814	X-RAY DIFFRACTION	95
2.4263-2.487	0.189	158	0.1748	46658	X-RAY DIFFRACTION	97
2.487-2.5543	0.2063	158	0.1653	47332	X-RAY DIFFRACTION	98
2.5543-2.6294	0.2028	156	0.1636	47613	X-RAY DIFFRACTION	99
2.6294-2.7142	0.1675	158	0.1611	47766	X-RAY DIFFRACTION	99
2.7142-2.8112	0.1755	158	0.1588	47682	X-RAY DIFFRACTION	99
2.8112-2.9238	0.1824	157	0.1553	47620	X-RAY DIFFRACTION	98
2.9238-3.0568	0.1918	160	0.1529	47554	X-RAY DIFFRACTION	98
3.0568-3.2179	0.1719	158	0.1486	48103	X-RAY DIFFRACTION	100
3.2179-3.4194	0.1772	157	0.1389	48171	X-RAY DIFFRACTION	100
3.4194-3.6832	0.1797	163	0.1245	48030	X-RAY DIFFRACTION	99
3.6832-4.0535	0.136	157	0.1178	47911	X-RAY DIFFRACTION	99
4.0535-4.6393	0.1258	159	0.1072	47672	X-RAY DIFFRACTION	99
4.6393-5.8421	0.1377	158	0.1115	48253	X-RAY DIFFRACTION	100
5.8421-39.7843	0.1664	157	0.155	47428	X-RAY DIFFRACTION	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	0.48	0.1778	0.0841	0.5085	0.1051	0.5012	0.0262	-0.0825	0.0494	0.0216	-0.0221	0.0761	-0.0129	-0.0871	-0.0045	0.1492	-0.0184	0.0056	0.192	-0.0039	0.1687	-75.4588	28.626	255.8283
2	1.2747	-0.1954	0.665	0.5693	-0.2581	1.5863	0.0968	-0.1189	-0.1114	0.0165	-0.0107	0.169	0.1089	-0.3761	-0.0685	0.1598	-0.0566	-0.025	0.2551	0.0039	0.1975	-95.9611	10.4384	233.3736
3	0.3829	0.1227	-0.0397	0.4804	-0.0362	0.6566	-0.0262	0.0276	-0.041	-0.047	0.0263	-0.0176	0.0332	0.0208	-0.0022	0.1496	-0.0171	0.0073	0.1233	-0.0067	0.142	-40.8098	16.0059	226.2866
4	0.3817	0.1998	-0.2	1.1334	-0.3826	0.4504	-0.0941	0.0675	-0.1256	-0.1679	0.0399	-0.0723	0.1691	-0.0031	0.0497	0.2212	-0.0405	0.037	0.1492	-0.0111	0.2184	-56.2593	-14.9385	234.4874
5	0.6507	-0.0839	-0.0526	0.5048	0.0115	0.5996	0.0267	0.1187	0.0888	-0.1226	-0.0458	-0.0309	-0.0366	0.0722	0.0167	0.174	0.0125	0.008	0.1746	0.0189	0.1585	-71.436	-52.9982	233.5919
6	0.41	-0.0101	-0.166	0.6998	-0.3621	1.3306	-0.0026	0.0581	-0.0954	-0.1592	-0.07	-0.02	0.2031	0.0939	0.076	0.209	0.0394	0.0121	0.1605	-0.0155	0.1756	-69.3684	-74.3964	234.5061
7	1.2918	-0.9103	0.1981	1.4256	-0.3166	0.4732	-0.0392	-0.083	-0.0964	0.0688	0.0383	0.1227	0.066	-0.033	-0.0043	0.1582	-0.0007	0.0107	0.1565	0.0022	0.1514	-80.3534	-64.6653	253.811
8	1.562	0.0914	0.0539	0.7776	0.0858	0.6847	-0.0054	0.0905	0.0968	-0.1314	-0.0725	0.2199	-0.0667	-0.1761	0.0705	0.1715	0.0492	-0.0452	0.1979	-0.0257	0.2499	-102.0084	-42.1709	240.2718
9	0.796	-0.0838	-0.3479	0.5907	-0.0454	0.7696	-0.0349	-0.0954	-0.0438	0.1052	0.0001	-0.0377	0.1193	0.0886	0.0339	0.1907	0.027	0.005	0.1694	0.0347	0.1666	-132.9531	4.3786	213.339
10	0.8873	-0.0939	-0.1895	0.6501	-0.0884	1.8232	0.0201	0.0802	0.0713	0.0441	0.0502	0.0856	0.0013	-0.2362	-0.0634	0.1843	0.0111	0.0265	0.2275	0.0456	0.2239	-152.116	10.3778	205.4329
11	0.9743	-0.7069	-0.0972	1.683	-0.1665	0.635	0.0323	0.2281	-0.0257	-0.1713	-0.0498	0.0021	0.101	-0.0183	0.0191	0.1962	0.0253	0.0123	0.2284	0.0244	0.1651	-133.5117	4.0929	188.2376
12	0.8397	0.2808	-0.4846	1.1481	0.2332	1.1256	-0.2115	-0.0315	-0.3621	0.0902	0.0015	-0.0959	0.3871	0.0667	0.1679	0.3795	0.1014	0.0965	0.1946	0.0381	0.3554	-120.3221	-23.956	200.3737
13	0.6109	-0.1959	-0.0731	0.5555	0.0621	0.685	-0.0265	-0.1032	0.041	0.1084	0.0686	-0.0348	-0.0533	0.0585	-0.0432	0.1943	0.0205	0.02	0.192	-0.0014	0.1681	-35.116	-62.8313	197.4909
14	0.3254	0.0039	-0.1347	1.1414	-0.0133	0.7923	0.0519	-0.0368	0.1863	0.0038	0.0526	0.0331	-0.4036	-0.0197	-0.0984	0.3696	0.0303	0.062	0.1831	0.0171	0.2336	-46.7088	-35.8969	177.9285
15	0.9577	-0.2906	0.0752	1.3108	-0.147	0.8167	0.0705	-0.1843	0.0565	0.0354	-0.021	-0.0516	-0.1214	0.072	-0.05	0.1456	-0.028	0.0227	0.2099	-0.0401	0.0997	-112.3719	-66.9247	186.5993
16	0.6283	0.0824	-0.1264	0.591	-0.1602	0.7283	0.0793	-0.1871	0.0847	0.0822	-0.0343	0.007	-0.0819	0.0758	-0.0437	0.1698	-0.0425	0.015	0.2543	-0.0332	0.1704	-118.6692	-72.844	198.7461
17	0.7628	0.089	-0.0205	0.6268	0.1035	0.6649	0.0246	-0.0922	-0.0672	0.0563	-0.0226	0.0203	0.0725	-0.032	0.0018	0.1614	-0.0335	-0.002	0.2212	0.003	0.1728	-126.4497	-90.6796	192.3887
18	3.9088	2.6555	-0.2533	2.8168	-0.2152	1.1357	0.0492	0.1323	-0.203	-0.062	0.0071	-0.185	0.1368	0.1316	-0.0581	0.1698	0.0069	-0.0302	0.1865	-0.0252	0.1398	-115.4775	-89.644	170.3291
19	2.1183	0.4866	0.3851	0.422	0.1272	0.475	0.0116	0.0198	-0.0025	-0.026	0.0132	-0.0316	-0.02	0.0667	-0.0324	0.1493	-0.0226	0.0106	0.1903	-0.0157	0.1468	-111.4386	-77.5595	176.0622
20	3.2397	-1.5158	0.4522	1.373	-0.1831	1.0873	0.1108	0.0243	-0.2467	-0.0087	-0.0824	0.1453	0.0717	0.1247	-0.0309	0.1266	-0.0312	0.0025	0.2416	-0.0197	0.1351	-89.7031	-77.606	176.6532
21	2.7304	0.7525	0.0976	3.2063	-2.1375	4.3786	0.0485	-0.149	-0.3463	0.0365	-0.1233	-0.1155	0.1836	0.0982	0.075	0.093	0.0083	0.0288	0.2367	-0.0101	0.2021	-80.9639	-82.7202	181.2494
22	0.5585	0.2223	0.8915	2.4518	1.1501	1.8028	0.0322	-0.2023	-0.048	0.1226	-0.0013	-0.1248	0.0954	0.1486	-0.0394	0.1613	-0.0375	-0.0044	0.4048	0.0414	0.2376	-74.0609	-77.3214	189.7341
23	3.146	-0.7222	0.1269	0.4313	0.3053	0.5034	0.0545	-0.5346	-0.2025	0.1705	-0.1576	-0.0031	-0.0129	0.1663	0.1339	0.2159	-0.0899	-0.0163	0.4317	-0.018	0.1935	-80.7346	-70.6671	198.2006
24	1.5271	-0.0748	0.086	0.4395	-0.1138	0.7379	0.066	-0.3253	0.1939	0.142	-0.0447	-0.0579	-0.234	0.1641	-0.0008	0.2229	-0.1033	0.0208	0.3264	-0.0793	0.2019	-90.1003	-59.1004	194.1842
25	0.6126	-0.2412	-0.2412	0.5221	0.0482	0.8747	0.0568	0.0116	0.0234	-0.0777	-0.0474	-0.0451	-0.0099	0.1142	-0.0067	0.134	0.0137	-0.0055	0.21	0.0163	0.1404	-107.548	22.4681	166.0884
26	1.5053	-0.5864	0.2819	0.6999	-0.2473	1.1239	-0.0367	-0.2832	0.0303	0.148	0.0637	-0.0422	-0.072	0.1121	-0.0232	0.1436	0.0012	-0.0019	0.2544	0.0016	0.1402	-113.3169	24.1389	188.4154
27	2.9104	-0.8678	0.4486	1.0781	0.113	0.6253	-0.115	-0.2531	0.3268	0.1484	0.0896	-0.2764	-0.1249	0.5578	0.0435	0.2919	-0.0025	-0.066	0.7489	-0.0447	0.3036	-83.0292	20.2036	201.6203
28	1.7936	-0.1214	0.5679	0.6425	0.4286	0.7698	-0.1061	-0.2679	-0.2415	0.0379	0.0433	-0.1558	0.2141	0.4984	0.0245	0.2439	0.1533	0.0104	0.5902	0.0983	0.2672	-85.8829	1.3273	188.6249
29	0.4368	-0.0559	-0.0898	1.4917	-0.0553	0.8605	-0.0091	-0.0037	0.0275	0.1723	0.0206	0.1774	-0.0451	-0.0854	-0.0114	0.1888	0.0092	0.0344	0.1282	0.0013	0.1785	-83.0938	-43.5899	281.1765
30	0.699	-0.3439	-0.1335	1.0716	0.0301	0.431	-0.0716	-0.1309	0.0097	0.3709	0.0519	-0.0086	0.0144	0.0335	0.0209	0.3402	0.0207	-0.0135	0.1718	-0.0013	0.1636	-69.8324	-54.4752	295.2889
31	1.8313	-1.6973	1.0602	3.3798	-1.7455	2.3823	0.0032	0.0863	0.1301	-0.0494	-0.0629	-0.3774	0.0349	0.2174	0.061	0.1684	0.0112	0.0063	0.1304	-0.0115	0.1954	-56.249	-55.1494	271.731
32	0.1825	-0.3086	0.0689	2.857	-0.7044	0.2779	0.0177	0.044	-0.0007	-0.0639	-0.0583	-0.0941	0.0275	0.0595	0.0389	0.1887	0.0074	0.0138	0.1383	-0.0017	0.1733	-67.841	-45.1872	268.5838
33	1.2239	-0.1149	-0.4335	2.0958	0.4397	1.1729	-0.0258	-0.1311	-0.0095	0.1633	-0.0309	-0.2394	-0.0792	0.1485	0.0574	0.2135	-0.0294	-0.0286	0.1388	0.033	0.2062	-61.8579	-14.9211	269.1101
34	0.4296	0.2618	-0.2759	1.7742	-0.4498	0.9281	0.015	-0.0143	0.1409	0.1824	0.0211	0.183	-0.1667	-0.086	-0.0298	0.1877	0.0285	0.0182	0.1108	-0.0011	0.2031	-84.143	-18.5661	272.3881

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 446 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 447 through 745 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid -1 through 406 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 407 through 745 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid -1 through 167 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 168 through 312 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 313 through 446 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 447 through 745 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid -1 through 167 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 168 through 312 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 313 through 466 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 467 through 745 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid -1 through 406 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 407 through 745 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid -1 through 39 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 40 through 167 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 168 through 312 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 313 through 361 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 362 through 446 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 447 through 500 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 501 through 545 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 546 through 589 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 590 through 637 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 638 through 745 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid -1 through 312 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 313 through 471 )
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 472 through 609 )
28	X-RAY DIFFRACTION	28	chain 'G' and (resid 610 through 745 )
29	X-RAY DIFFRACTION	29	chain 'H' and (resid -1 through 110 )
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 111 through 312 )
31	X-RAY DIFFRACTION	31	chain 'H' and (resid 313 through 361 )
32	X-RAY DIFFRACTION	32	chain 'H' and (resid 362 through 466 )
33	X-RAY DIFFRACTION	33	chain 'H' and (resid 467 through 609 )
34	X-RAY DIFFRACTION	34	chain 'H' and (resid 610 through 745 )

-
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

-
Protein , 1 types, 8 molecules ABCDEFGH

-
Non-polymers , 6 types, 9698 molecules

-
Details

-
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

-Protein , 1 types, 8 molecules ABCDEFGH

-Non-polymers , 6 types, 9698 molecules

-Details

-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

-
Protein , 1 types, 8 molecules ABCDEFGH

-
Non-polymers , 6 types, 9698 molecules

-
Details

-
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