PDB-5ej9: EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min an...

ID or keywords:

Entry

Database: PDB / ID: 5ej9

Title

EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and isochorismate for 13 min

Components

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

Keywords

TRANSFERASE / Post-decarboxylation intermediate

Function / homology

Function and homology information

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity / menaquinone biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / magnesium ion binding / protein homodimerization activity
Similarity search - Function

Biological species

Escherichia coli K12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.72 Å

Authors

Song, H.G. / Dong, C. / Chen, Y.Z. / Sun, Y.R. / Guo, Z.H.

Citation

Journal: J.Am.Chem.Soc. / Year: 2016
Title: A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
Authors: Song, H.G. / Dong, C. / Qin, M.M. / Chen, Y.Z. / Sun, Y.R. / Liu, J.J. / Chan, W. / Guo, Z.H.

History

Deposition	Nov 1, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jun 1, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 29, 2016	Group: Database references
Revision 1.2	Nov 8, 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_oper_list / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ej9.cif.gz	1.7 MB	Display	PDBx/mmCIF format
PDB format	pdb5ej9.ent.gz	1.4 MB	Display	PDB format
PDBx/mmJSON format	5ej9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5ej9_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	5ej9_full_validation.pdf.gz	2.7 MB	Display
Data in XML	5ej9_validation.xml.gz	203.3 KB	Display
Data in CIF	5ej9_validation.cif.gz	306.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ej/5ej9 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/5ej9	HTTPS FTP

-
Related structure data

Related structure data	5ej4C 5ej5C 5ej6C 5ej7C 5ej8C 5ejaC 2jlcS 5ejm C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ej8-1 5ej4-3 5ej4-1 5ej4-4 5ej6-1 5eja-1 2jla-2 5ej7-3 5ej5-2 3hwx-4 3hwx-3 5ej8-4 5eja-4 5ej8-2 5ejm-2 3hwx-2 5ejm-3 5ej5-1 5ej6-4 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

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	#263 - Nov 2021 Acetohydroxyacid Synthase similarity (6) #153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (2) #154 - Oct 2012 Citric Acid Cycle similarity (1)

Deposited unit

A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

B: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

C: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

D: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

E: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

F: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

G: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

H: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

hetero molecules

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

1

A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

B: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

hetero molecules

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

2

C: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

D: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

hetero molecules

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

3

E: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

F: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

hetero molecules

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

4

G: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

H: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	90.720, 90.720, 169.470
Angle α, β, γ (deg.)	76.06, 83.35, 64.38
Int Tables number	1
Space group name H-M	P1

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / ThDP-dependent enzyme MenD / SEPHCHC synthase / Menaquinone biosynthesis protein MenD Mass: 61433.781 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K12 substr. MG1655 / Gene: menD, b2264, JW5374 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P17109, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase

#1: Protein

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / ThDP-dependent enzyme MenD / SEPHCHC synthase / Menaquinone biosynthesis protein MenD

Mass: 61433.781 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli K12 (bacteria) / Strain: K12 substr. MG1655 / Gene: menD, b2264, JW5374 / Plasmid: pET28a / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P17109, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase

-
Non-polymers , 5 types, 5429 molecules

#2: Chemical	ChemComp-TPP / THIAMINE DIPHOSPHATE Mass: 425.314 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₂H₁₉N₄O₇P₂S
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH₂O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 5397 / 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: 2.48 Å³/Da / Density % sol: 50.47 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.16 M magnesium formate, 1% tascimate pH 7.0, 0.02 M HEPES pH 7.0, 14% PEG 3350 and 2% PEG MME 5000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.72→41.85 Å / Num. obs: 487194 / % possible obs: 96.5 % / Redundancy: 2 % / R_merge(I) obs: 0.048 / Net I/σ(I): 8.1
Reflection shell	Resolution: 1.72→1.75 Å / Redundancy: 2 % / R_merge(I) obs: 0.156 / Mean I/σ(I) obs: 3.1 / % possible all: 91.2

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2JLC

2jlc

Resolution: 1.72→39.961 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 16.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.182	23965	4.92 %
R_work	0.1507	-	-
obs	0.1522	487181	96.48 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.72→39.961 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	34385	0	288	5397	40070

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	35930
X-RAY DIFFRACTION	f_angle_d	1.067	49100
X-RAY DIFFRACTION	f_dihedral_angle_d	12.441	12911
X-RAY DIFFRACTION	f_chiral_restr	0.045	5442
X-RAY DIFFRACTION	f_plane_restr	0.005	6408

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 (%)
1.717-1.7365	0.2191	744	0.1834	14250	X-RAY DIFFRACTION	89
1.7365-1.7569	0.2353	789	0.1824	15295	X-RAY DIFFRACTION	95
1.7569-1.7784	0.2231	803	0.1759	15378	X-RAY DIFFRACTION	96
1.7784-1.8009	0.2166	770	0.1697	15199	X-RAY DIFFRACTION	96
1.8009-1.8246	0.198	783	0.1606	15406	X-RAY DIFFRACTION	96
1.8246-1.8496	0.2049	820	0.1633	15373	X-RAY DIFFRACTION	96
1.8496-1.876	0.1974	810	0.1613	15070	X-RAY DIFFRACTION	96
1.876-1.904	0.2004	769	0.1606	15482	X-RAY DIFFRACTION	96
1.904-1.9337	0.1976	797	0.1594	15472	X-RAY DIFFRACTION	96
1.9337-1.9654	0.203	830	0.1588	15299	X-RAY DIFFRACTION	96
1.9654-1.9993	0.2041	840	0.1607	15303	X-RAY DIFFRACTION	96
1.9993-2.0357	0.2013	873	0.1571	15278	X-RAY DIFFRACTION	96
2.0357-2.0748	0.1952	788	0.1574	15564	X-RAY DIFFRACTION	97
2.0748-2.1172	0.1867	792	0.1539	15399	X-RAY DIFFRACTION	96
2.1172-2.1632	0.1835	787	0.1531	15564	X-RAY DIFFRACTION	97
2.1632-2.2135	0.1932	745	0.1569	15513	X-RAY DIFFRACTION	97
2.2135-2.2689	0.1984	835	0.1545	15481	X-RAY DIFFRACTION	97
2.2689-2.3302	0.1909	829	0.1522	15493	X-RAY DIFFRACTION	97
2.3302-2.3988	0.1838	841	0.15	15497	X-RAY DIFFRACTION	97
2.3988-2.4762	0.1966	814	0.1545	15489	X-RAY DIFFRACTION	97
2.4762-2.5647	0.1854	809	0.1509	15578	X-RAY DIFFRACTION	97
2.5647-2.6674	0.1845	756	0.1514	15657	X-RAY DIFFRACTION	97
2.6674-2.7887	0.1924	757	0.1539	15585	X-RAY DIFFRACTION	98
2.7887-2.9357	0.1739	860	0.1494	15668	X-RAY DIFFRACTION	98
2.9357-3.1196	0.1738	801	0.1465	15642	X-RAY DIFFRACTION	98
3.1196-3.3603	0.1663	818	0.1422	15649	X-RAY DIFFRACTION	98
3.3603-3.6983	0.1691	802	0.1409	15515	X-RAY DIFFRACTION	97
3.6983-4.2329	0.1623	754	0.1355	15557	X-RAY DIFFRACTION	97
4.2329-5.331	0.1541	722	0.1353	15768	X-RAY DIFFRACTION	98
5.331-39.9718	0.1565	827	0.1543	15792	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	0.4103	-0.3052	-0.1064	0.5825	0.0431	0.4861	0.0262	0.0036	-0.0097	-0.0241	-0.0146	0.0447	0.0138	-0.0435	-0.0096	0.1182	-0.0219	-0.0074	0.0671	-0.0127	0.1115	-44.3641	1.0721	-23.0157
2	3.5341	0.9443	-0.2779	0.4215	-0.0865	0.0305	-0.0131	0.0186	0.2086	-0.0234	0.0214	0.0372	-0.0592	0.0062	-0.0074	0.1618	-0.0154	-0.0215	0.0983	-0.0138	0.1511	-37.4506	22.1378	-25.2632
3	0.3402	-0.0154	0.1209	1.0083	0.5808	0.7674	-0.001	0.0474	0.0581	-0.0514	0.017	-0.1669	-0.0396	0.1432	-0.0077	0.1071	-0.0285	0.0221	0.098	0.0124	0.1384	-7.7785	13.3015	-34.0855
4	0.4817	-0.1134	-0.0301	0.4209	0.0195	0.4949	0.0044	0.0343	-0.019	-0.0184	-0.0055	-0.0657	0.0608	0.0718	-0.0056	0.1415	0.0034	0.0193	0.0929	-0.0057	0.1156	-16.8815	-8.7071	-39.6439
5	0.3745	-0.0624	0.1047	0.4681	-0.046	0.6951	0.0026	-0.0097	-0.0081	0.0071	0.0085	-0.0586	0.074	0.0538	-0.0108	0.1235	-0.0064	-0.006	0.0607	-0.0066	0.107	-17.9679	-13.3165	-9.972
6	2.7347	0.8574	-0.4276	0.4022	-0.1972	0.3493	0.0062	-0.0978	-0.2006	0.0506	-0.0294	-0.0398	0.1438	0.0119	0.0192	0.2086	-0.0053	-0.0191	0.0834	-0.0144	0.1456	-26.3643	-24.1498	7.2533
7	0.1962	0.0211	-0.0482	0.481	0.2482	0.8559	-0.0009	0.0125	-0.0408	-0.0001	0.0115	0.0767	0.0828	-0.0854	-0.0143	0.1675	-0.0506	-0.0079	0.0794	-0.002	0.1641	-53.4603	-32.1968	-8.7926
8	0.3103	0.1753	0.0419	0.2508	-0.1137	0.3827	0.0051	0.0281	-0.0538	-0.0733	0.0111	0.0266	0.0976	-0.0416	-0.0142	0.2035	-0.0369	-0.019	0.0789	-0.0158	0.1406	-40.9914	-27.9808	-29.5762
9	0.4985	-0.0632	-0.1893	0.5634	0.0541	0.6117	0.0172	-0.0349	0.0109	0.0464	-0.0075	-0.0723	-0.0333	0.0719	-0.0048	0.1264	-0.0272	-0.0214	0.0759	-0.0109	0.1135	-18.9809	14.9075	3.3292
10	2.4521	-0.8727	1.025	0.4008	-0.512	0.7444	-0.0777	0.0442	0.1422	0.0126	0.0151	-0.1115	-0.1695	0.0531	0.0501	0.1752	-0.0389	-0.0046	0.0754	-0.0253	0.1398	-22.5583	26.6202	-16.2259
11	0.3812	-0.1639	-0.1384	0.6102	0.462	1.1883	-0.0064	-0.0014	0.0363	-0.0103	-0.0208	0.0727	-0.1715	-0.0846	0.0276	0.1664	0.009	-0.0109	0.058	-0.0082	0.1217	-51.1812	36.0825	-7.8709
12	0.2876	0.0568	-0.0407	0.6295	0.0003	0.3251	-0.024	-0.0627	0.0318	0.099	0.0205	0.0009	-0.0805	-0.0314	0.0044	0.1964	0.0085	0.0034	0.0863	-0.0155	0.1004	-43.4573	29.0356	15.1898
13	1.8287	-0.3296	0.3681	0.4395	0.1666	0.9474	-0.1281	-0.2133	0.1459	0.1122	0.0643	0.0702	-0.117	-0.0655	0.0718	0.2389	0.0233	0.0233	0.0834	-0.0172	0.1394	-51.4469	38.19	16.4048
14	0.3939	0.0954	0.0343	0.4523	0.0627	0.6798	-0.0045	-0.024	-0.0248	0.052	0.006	0.0611	0.0055	-0.0479	-0.006	0.1426	-0.0146	0.0111	0.0748	0.0005	0.1138	-49.0006	2.5743	7.966
15	2.7406	-1.0665	0.6602	0.8649	-0.2549	0.4687	-0.0481	-0.1228	-0.1777	0.1904	0.0603	0.0959	0.1113	-0.0517	-0.046	0.2616	-0.0395	0.0113	0.1156	0.0069	0.1485	-44.6557	-18.7766	11.9517
16	0.4773	0.0019	-0.06	0.7307	0.313	1.0793	-0.033	-0.158	-0.0954	0.2904	0.0811	-0.0815	0.1916	0.1435	-0.0309	0.2745	0.0428	-0.0454	0.1456	0.0128	0.1302	-18.0956	-15.7251	25.2772
17	0.7878	-0.3847	0.1575	0.7076	0.4161	0.7373	-0.1365	-0.1953	0.0046	0.2024	0.159	-0.1464	0.159	0.2174	-0.012	0.3688	0.0486	-0.0737	0.2509	-0.005	0.1364	-17.9415	0.1028	41.6693
18	0.4196	-0.0497	0.1724	0.6223	0.0791	0.6626	-0.054	-0.1281	0.0109	0.1876	0.0608	-0.0715	-0.0159	0.0588	-0.0123	0.2572	0.0077	-0.0336	0.1577	-0.0091	0.1012	-26.9079	10.5702	31.9322
19	0.4066	-0.227	-0.0715	0.7468	0.1452	0.5105	-0.0389	-0.0143	-0.0324	0.0457	0.0479	0.0237	0.0364	-0.0414	-0.0105	0.0666	0.0021	0.0103	0.1281	0.0057	0.1081	-50.5727	10.7836	-68.3705
20	1.376	1.4126	0.1876	1.6952	0.2153	0.1768	0.0496	-0.0374	-0.046	0.0725	-0.0344	-0.1221	0.0334	0.0536	-0.0203	0.1019	0.0281	0.0134	0.1458	0.014	0.1524	-28.7047	7.8331	-66.0159
21	0.6468	-0.3835	-0.3467	0.8845	0.1485	1.1553	-0.0071	-0.0391	0.098	0.0155	0.0084	-0.0899	-0.0864	0.0818	0.0085	0.0624	-0.0202	-0.0099	0.1244	-0.0106	0.1454	-20.7469	36.126	-60.9023
22	0.841	-0.1568	-0.2727	0.6554	0.184	0.6861	0.0336	-0.1203	0.1772	0.1965	0.0641	-0.1526	-0.191	0.137	-0.0384	0.1784	-0.0077	-0.0378	0.1334	-0.0574	0.1487	-33.4491	46.1932	-44.889
23	0.3516	-0.0352	-0.0444	0.4554	0.09	0.4893	0.0039	-0.0093	0.066	0.0537	0.0045	-0.0011	-0.0988	-0.0324	-0.0134	0.1193	0.02	-0.004	0.1264	-0.0184	0.1265	-47.4179	39.819	-51.6807
24	0.504	-0.0374	0.0011	0.3375	-0.1249	0.7498	0.0145	0.0213	0.0507	-0.0151	0.0025	-0.0142	-0.0809	-0.0553	-0.0145	0.077	0.0238	0.0093	0.1194	0.0071	0.1138	-52.0785	40.8693	-81.319
25	0.9482	0.9793	0.2948	1.2866	0.2338	0.3192	-0.0168	0.085	0.1277	-0.047	0.0014	0.1584	-0.0538	-0.0841	0.0101	0.1203	0.0375	0.0091	0.1865	0.0109	0.1494	-65.4488	38.0396	-98.5435
26	0.5179	-0.1138	-0.2919	0.2805	0.2295	0.8855	-0.0046	0.009	-0.0446	0.0117	0.0035	0.0556	0.0483	-0.0942	0.0002	0.062	-0.0013	-0.0004	0.192	0.011	0.163	-84.4905	16.9732	-82.4019
27	0.4653	0.0842	0.0469	0.28	-0.0722	0.3228	-0.0047	-0.0786	-0.0052	0.0603	0.0198	0.0727	-0.0041	-0.1042	-0.0115	0.0832	0.0188	0.0227	0.2087	0.0085	0.1362	-75.2288	26.5098	-61.7487
28	0.375	-0.0388	0.0005	0.5239	0.155	0.5384	-0.0013	0.0546	0.0497	-0.0374	0.0158	-0.0461	-0.051	0.0444	-0.0163	0.0768	-0	0.0134	0.1553	0.0136	0.1224	-27.1299	27.6877	-94.6663
29	0.0396	0.2667	-0.094	3.2839	-1.3725	0.8402	0.0152	-0.024	0.0417	0.0341	-0.0842	-0.1692	0.0216	0.1693	0.0607	0.0841	0.0178	0.0001	0.1961	-0.0054	0.154	-18.0389	19.4239	-75.1384
30	0.4753	-0.2068	-0.4023	0.5862	0.3274	1.2473	-0.0335	-0.012	-0.0858	0.0216	-0.014	0.0089	0.165	0.1233	0.0449	0.0867	0.036	0.009	0.1351	0.0099	0.1024	-21.7584	-10.545	-83.421
31	0.3306	-0.0793	-0.0886	0.4791	-0.0886	0.462	0.0037	0.0693	-0.0344	-0.0998	-0.0106	-0.0462	0.0744	0.0336	0.0104	0.1273	0.0332	0.0144	0.1838	-0.009	0.1212	-23.7636	-3.3058	-106.8306
32	0.5564	-0.0476	-0.1123	0.4307	-0.0779	0.5935	0.0148	0.0627	-0.0274	-0.0327	-0.017	0.0494	0.0439	-0.0558	0.0001	0.0789	0.0027	-0.0021	0.1572	-0.0053	0.1099	-51.176	5.9784	-99.281
33	0.2735	0.1432	-0.0833	2.9139	-0.8119	0.5833	0.0668	0.1419	0.0206	-0.1296	-0.0169	0.2493	-0.026	-0.1709	-0.0687	0.0955	0.0342	0.0044	0.2643	-0.0005	0.1571	-68.5225	19.1941	-103.1758
34	0.9437	-0.114	-0.1445	0.505	0.1924	1.3216	0.0612	0.1996	0.1547	-0.1157	-0.0073	-0.0016	-0.1518	-0.1319	-0.0411	0.154	0.0566	0.0143	0.2071	0.0521	0.1267	-54.1617	41.8419	-116.5945
35	0.4001	-0.0511	-0.0022	0.5301	-0.1492	0.5874	0.0335	0.1042	0.066	-0.1591	-0.0199	-0.0306	-0.0449	0.0312	-0.0135	0.1546	0.0292	0.0231	0.2338	0.03	0.103	-35.4756	24.6106	-124.9925

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 182 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 183 through 219 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 220 through 384 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 385 through 556 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 182 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 183 through 219 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 220 through 384 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 385 through 556 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1 through 182 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 183 through 219 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 220 through 384 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 385 through 513 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 514 through 556 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 1 through 182 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 183 through 219 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 220 through 347 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 348 through 384 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 385 through 556 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 1 through 182 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 183 through 219 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 220 through 347 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 348 through 384 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 385 through 556 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 1 through 182 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 183 through 219 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 220 through 384 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 385 through 556 )
28	X-RAY DIFFRACTION	28	chain 'G' and (resid 1 through 182 )
29	X-RAY DIFFRACTION	29	chain 'G' and (resid 183 through 219 )
30	X-RAY DIFFRACTION	30	chain 'G' and (resid 220 through 384 )
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 385 through 556 )
32	X-RAY DIFFRACTION	32	chain 'H' and (resid 1 through 182 )
33	X-RAY DIFFRACTION	33	chain 'H' and (resid 183 through 219 )
34	X-RAY DIFFRACTION	34	chain 'H' and (resid 220 through 347 )
35	X-RAY DIFFRACTION	35	chain 'H' and (resid 348 through 556 )

-
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

-
Protein , 1 types, 8 molecules ABCDEFGH

-
Non-polymers , 5 types, 5429 molecules

-
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 , 5 types, 5429 molecules

-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 , 5 types, 5429 molecules

-
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