PDB-3lor: The Crystal Structure of a Thiol-disulfide Isomerase from Coryneb...

ID or keywords:

Entry

Database: PDB / ID: 3lor

Title

The Crystal Structure of a Thiol-disulfide Isomerase from Corynebacterium glutamicum to 2.2A

Components

Thiol-disulfide isomerase and thioredoxins

Keywords

ISOMERASE / Thiol / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative

Function / homology

Function and homology information

isomerase activity / oxidoreductase activity / metal ion binding
Similarity search - Function

Biological species

Corynebacterium glutamicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.2 Å

Authors

Stein, A.J. / Osipiuk, J. / Weger, A. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The Crystal Structure of a Thiol-disulfide Isomerase from Corynebacterium glutamicum to 2.2A
Authors: Stein, A.J. / Osipiuk, J. / Weger, A. / Cobb, G. / Joachimiak, A.

History

Deposition	Feb 4, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 16, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3lor.cif.gz	139 KB	Display	PDBx/mmCIF format
PDB format	pdb3lor.ent.gz	113.9 KB	Display	PDB format
PDBx/mmJSON format	3lor.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lo/3lor ftp://data.pdbj.org/pub/pdb/validation_reports/lo/3lor	HTTPS FTP

-
Related structure data

Similar structure data	4v4f-2 1881 1utd-1 3aqd-2 4v4f-4 3aqd-1 4j5s-d 1pt9-3 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	TargetDB: APC61551

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Thiol-disulfide isomerase and thioredoxins

B: Thiol-disulfide isomerase and thioredoxins

C: Thiol-disulfide isomerase and thioredoxins

D: Thiol-disulfide isomerase and thioredoxins

hetero molecules

73.4 kDa, 4 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)	78.190, 78.892, 124.229
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

Biological unit is the same as asymmetric unit.

#1: Protein	Thiol-disulfide isomerase and thioredoxins Mass: 18277.035 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC 13932 / Gene: cg1043, Cgl0914 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NRX7
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.66 Å³/Da / Density % sol: 53.9 %
Crystal grow	Temperature: 277 K / pH: 4.6 Details: 30% MPD, 0.1M Sodium acetate pH 4.6, 0.2M Calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 19, 2009
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 45076 / % possible obs: 99.5 % / Redundancy: 4.9 % / R_merge(I) obs: 0.115 / Net I/σ(I): 8
Reflection shell	Resolution: 2.1→2.18 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.784 / % possible all: 100

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
SHELX		phasing
MLPHARE		phasing
DM		phasing
ARP/wARP		model building
Coot		model building

Refinement

Resolution: 2.2→41.4 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.913 / SU B: 14.493 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.259	1974	5 %	RANDOM
R_work	0.212	-	-	-
obs	0.214	39504	99.4 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 14.65 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	-0.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→41.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4723	0	10	96	4829

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	4856
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.303	1.965	6588
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.976	5	618
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.587	24.372	215
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.468	15	847
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.62	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	763
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	3640
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.467	1.5	3051
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.866	2	4943
X-RAY DIFFRACTION	r_scbond_it	1.724	3	1805
X-RAY DIFFRACTION	r_scangle_it	2.685	4.5	1639
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.2→2.26 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.306	133	-
R_work	0.264	2751	-
obs	-	-	99.72 %

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	26.1407	-5.8648	7.7607	1.8092	-1.7852	2.4813	0.5135	2.2175	-0.824	-0.6058	-0.3187	0.3164	0.1365	0.4785	-0.1948	0.5395	-0.0565	-0.1061	0.3961	-0.045	0.2513	-30.7083	3.1065	-26.9023
2	19.4135	-5.847	2.3126	4.2197	0.1093	1.7038	-0.3969	-0.2203	-0.0204	-0.2028	0.2495	-0.1391	0.0754	0.1388	0.1473	0.2121	0.0522	0.1007	0.2177	0.0642	0.2333	-15.8357	2.9336	-18.6537
3	2.0105	-2.6726	-4.3156	18.7288	11.0162	20.008	-0.1668	-0.4017	0.1906	0.4159	0.7225	-0.7951	0.5589	0.8411	-0.5558	0.2136	0.0305	-0.111	0.3047	0.0437	0.1574	-11.7123	7.0048	-8.6878
4	17.3158	-0.8271	8.8493	2.237	-1.4874	5.1475	-0.5075	-0.7367	-0.5506	0.2826	0.3486	-0.6033	-0.4009	-0.4318	0.159	0.2923	0.0344	-0.0054	0.3482	0.0536	0.3234	-21.3015	2.0814	-9.2846
5	22.2519	4.7485	-9.2372	13.6397	-8.0599	7.0514	-0.3196	-0.2436	-0.641	-0.0232	0.2674	0.403	0.3416	-0.1986	0.0523	0.2834	-0.0196	0.0037	0.1885	-0.0576	0.1381	-27.2394	8.21	-13.5964
6	10.5321	7.2021	-1.297	8.941	1.1145	2.2202	0.3949	0.2404	0.4031	0.1912	-0.1593	-0.2424	0.0044	0.1312	-0.2356	0.166	0.0512	-0.0047	0.198	0.0172	0.1382	-10.1022	17.9007	-18.8989
7	20.9462	-0.2683	-0.1907	12.8659	0.5339	23.6096	0.2223	0.1076	1.0032	0.1303	0.1701	0.1321	-0.8516	0.2544	-0.3923	0.1786	-0.0207	-0.0088	0.1314	0.045	0.1632	-12.6871	25.623	-18.9004
8	10.3315	5.3113	-8.3755	8.7208	-1.6666	15.0494	0.1193	-0.1634	0.4771	0.1384	-0.1212	0.2024	-0.3864	-0.1702	0.002	0.185	0.0191	-0.0314	0.1404	-0.0141	0.1061	-19.8869	21.7953	-11.7131
9	9.6625	3.6912	0.492	20.4957	-0.8709	12.6939	0.3398	-0.2943	0.7099	0.5847	-0.1366	0.2434	-0.5478	0.0526	-0.2031	0.1641	0.046	0.0515	0.3048	-0.0271	0.0862	-27.3206	16.453	-6.478
10	9.2306	0.8176	-2.3178	0.5668	0.1551	1.85	0.1015	0.2136	-0.0207	-0.0772	0.0409	-0.173	-0.0656	0.1309	-0.1425	0.1864	0.0275	-0.0036	0.1032	-0.0279	0.1481	-9.8678	12.9674	-19.5057
11	2.0004	3.0008	-5.0775	10.6969	-6.4117	22.9598	-0.1043	0.0506	-0.0241	-0.4135	0.0076	0.0149	0.2111	0.4333	0.0966	0.15	0.0329	-0.0371	0.3055	-0.0194	0.3286	-0.052	13.2909	-15.9848
12	16.3389	-4.229	-6.8507	8.8986	2.9513	8.8366	0.0467	-0.1371	-0.0985	0.4832	-0.1335	-0.4534	-0.2595	0.2103	0.0868	0.2083	-0.008	-0.0834	0.1983	0.0151	0.1334	-7.2125	18.587	-8.292
13	7.9014	-2.0602	-6.727	1.7614	2.0188	9.6467	-0.212	-0.0518	-0.2998	0.1078	0.2033	-0.2346	0.3526	0.4664	0.0086	0.1378	0.0194	-0.0443	0.1222	-0.0143	0.196	-9.4189	7.7133	-20.4292
14	28.5758	0.3379	-3.2821	18.5593	-10.9173	19.8442	-0.0594	0.9447	-0.3412	-1.1983	-0.0353	-0.0984	0.7669	-0.2339	0.0948	0.1749	0.0279	0.0105	0.1893	-0.0818	0.0996	-16.2757	6.6836	-28.6462
15	17.1876	6.4591	-1.6275	8.144	3.4832	3.1522	0.083	0.7161	0.3801	-0.5573	0.1588	-0.0418	-0.3977	-0.1985	-0.2418	0.2188	0.0184	-0.0233	0.2029	0.0163	0.1201	-16.9046	15.901	-25.1318
16	9.1199	-0.4256	-6.7261	13.1501	-1.1088	10.7919	-0.4139	0.5598	-0.2526	-0.07	0.1854	1.3838	0.8684	-0.612	0.2286	0.1565	-0.0215	-0.0136	0.1931	-0.0231	0.2278	-31.2178	7.3694	-18.3841
17	25.46	14.4236	2.0084	8.3125	0.9103	1.7205	-0.1155	0.3985	1.4337	0.0922	0.1592	0.8804	-0.5173	-0.0114	-0.0437	0.2804	0.0499	0.0311	0.2137	0.0055	0.1649	-26.7972	13.0916	-24.9811
18	23.3265	-0.4634	3.3886	5.4271	0.8251	14.9816	-0.0593	0.1957	1.7542	-0.3898	0.3774	-0.4626	0.2172	0.1781	-0.318	0.1354	0.027	0.0494	0.1761	0.0606	0.3086	-21.5101	24.6973	-23.0794
19	3.8117	2.1795	-0.47	18.23	-7.3863	7.2952	-0.1017	0.2975	-0.2168	-0.1434	0.2359	-0.117	0.2626	0.064	-0.1343	0.1199	0.0255	0.0244	0.1694	-0.0031	0.1244	-31.0332	22.3849	-19.0823
20	7.5269	-7.5842	-3.8823	33.8158	2.0815	28.0809	0.3569	0.6834	-1.5384	-1.2495	-0.2509	2.1316	1.7892	-1.753	-0.106	0.2816	-0.0079	-0.1676	0.203	-0.0838	0.5778	-37.2868	12.9876	-16.9551
21	6.5789	4.2496	3.2817	22.8352	2.0967	2.3833	-0.284	-0.3925	0.6685	0.8798	0.0779	-0.3616	-0.2664	-0.0514	0.2061	0.1922	-0.0356	-0.1277	0.3718	-0.0044	0.1853	14.1275	46.6042	-7.9184
22	4.6804	-5.1471	0.098	6.2208	-3.5513	26.4992	-0.0341	-0.1112	-0.1951	-0.0067	0.2599	0.1681	0.656	-0.128	-0.2257	0.0954	-0.0028	-0.0629	0.1634	-0.0134	0.1471	13.5132	30.256	-18.1759
23	2.5325	0.4867	-0.7076	8.4991	-1.3204	0.4352	-0.2313	0.4616	-0.0119	-0.8466	0.0571	-1.0004	0.2526	-0.0168	0.1742	0.3372	0.0118	-0.0077	0.3171	0.0419	0.218	13.5441	41.1675	-21.9794
24	1.6452	-0.7131	1.2128	17.4984	-1.6405	1.2824	-0.1653	-0.0416	0.1011	-0.212	0.1881	-0.1879	-0.0745	-0.1161	-0.0228	0.173	0.0227	-0.0891	0.2175	0.0318	0.1283	4.442	40.0574	-14.9639
25	20.8951	-9.7483	3.1394	9.0861	-4.3332	3.1352	-0.0189	-0.4213	-0.7335	0.1073	0.2984	0.5219	-0.0018	-0.1459	-0.2795	0.1525	0.0066	-0.0332	0.1837	0.0379	0.1711	-4.8469	28.24	-11.9738
26	11.2667	6.5947	-3.3532	13.9652	-9.9429	11.3143	0.006	-0.014	0.0678	0.5652	0.1394	0.5384	-0.3592	-0.3834	-0.1455	0.148	0.0717	-0.0346	0.1852	-0.0293	0.1196	-5.2078	38.3863	-17.9815
27	2.4306	7.9054	1.4814	27.9093	-2.2929	36.7647	0.2338	-0.0661	0.4378	0.3241	-0.4946	1.5383	0.5765	-1.837	0.2608	0.2657	0.3154	-0.0763	0.676	-0.1549	0.1423	-1.9707	44.0144	-25.6733
28	12.7562	-2.2505	5.5949	0.9973	-5.4165	36.8086	-0.1592	0.4729	0.7633	0.0406	-0.1078	-0.1719	-0.3415	0.1855	0.267	0.1166	-0.0369	-0.0173	0.1749	0.0414	0.1581	5.1963	47.104	-24.0787
29	1.8929	-3.6006	2.5346	11.9137	-6.1435	6.2594	-0.1487	-0.3344	0.0045	0.1623	0.2514	0.2045	0.2877	-0.3968	-0.1028	0.1616	0.0119	-0.0558	0.1767	0.0034	0.0976	4.9407	29.6909	-10.4816
30	8.5751	-1.3804	-3.6679	2.9446	7.6701	31.9878	-0.1615	-0.4997	-0.4134	0.2592	-0.1076	0.5477	0.9435	-0.3694	0.2691	0.2493	-0.0332	-0.0453	0.2007	0.0261	0.2399	5.847	19.7649	-10.4337
31	1.8001	-1.2766	3.3451	7.0612	-9.9347	15.7766	0.1017	0.3436	-0.0226	-0.2701	-0.7446	-0.6741	0.6297	1.2329	0.6429	0.1736	-0.0175	-0.018	0.1946	-0.0251	0.5773	5.9346	22.582	-20.1378
32	19.1573	0.9951	6.9006	14.2695	-8.1737	25.8759	-0.4087	0.7717	-0.5791	-0.0181	0.3711	-0.2948	0.5798	-0.8293	0.0375	0.1251	0.0052	-0.0061	0.1724	-0.033	0.0675	-1.3581	27.4084	-22.8504
33	7.126	-3.488	4.4604	5.5108	-6.5851	14.5697	-0.0044	0.4813	0.1363	0.0253	-0.3379	-0.4528	0.1601	0.9037	0.3423	0.1109	0.0067	-0.0627	0.0997	-0.0106	0.1477	9.5791	31.6955	-15.3502
34	5.2055	-0.7452	0.5266	6.5915	-6.0531	11.5093	-0.0183	-0.3788	-0.3957	0.2855	-0.1588	0.0805	0.2046	0.1203	0.177	0.245	-0.0258	-0.003	0.2332	-0.001	0.1234	12.3551	27.9105	-2.944
35	29.1741	1.8351	-0.2957	20.6046	-2.3665	16.7255	0.2353	-1.2418	-0.0392	0.9133	-0.2476	-0.2989	-0.053	0.1659	0.0123	0.2059	0.039	-0.1014	0.2119	-0.0314	0.08	10.3237	37.5329	-2.4187
36	6.7605	4.261	-2.4031	11.8042	-5.0828	5.6019	0.2851	-0.4849	0.4555	0.9004	-0.1989	0.3119	-0.3903	0.1523	-0.0861	0.204	0.0446	-0.0419	0.1919	-0.0344	0.1165	4.6277	43.9748	-10.3175
37	16.0882	16.105	-1.0199	33.0311	-9.1044	13.328	-0.1348	-0.6726	0.2104	0.4902	-0.2014	-0.1903	-0.7149	0.1039	0.3363	0.261	0.0645	-0.1363	0.1795	-0.0572	0.1355	6.657	49.54	-7.8555
38	27.2801	2.0926	1.1758	22.4806	-3.3595	5.636	-0.128	-1.1966	0.3275	0.3363	0.3449	0.7624	-0.213	-0.1391	-0.2168	0.2269	0.1584	0.0737	0.4867	0.148	0.1906	-5.6119	40.7444	-6.758
39	21.073	5.1549	-1.9108	8.7491	-3.6161	1.5594	0.2335	-0.5304	0.0007	0.3129	-0.2751	-0.1959	-0.0993	0.0257	0.0417	0.204	0.0502	-0.0896	0.1891	-0.0295	0.164	-5.9511	49.7106	-13.3013
40	25.8804	0.9496	-2.4459	12.3524	-2.7203	24.8412	0.6514	-0.9766	1.5379	0.7917	-0.6313	0.1469	-1.5568	0.9354	-0.02	0.3	-0.0295	-0.1306	0.1579	-0.0748	0.3487	3.2541	57.2778	-15.7927
41	12.3301	-0.1465	2.2573	6.9078	-1.1326	0.6325	0.069	0.8013	0.0377	-0.0024	-0.1108	-0.5959	-0.0437	0.1936	0.0417	0.212	0.0211	-0.0061	0.2043	-0.0154	0.209	-16.5017	72.8503	-20.9314
42	12.651	5.5653	-5.3584	13.077	-1.4198	4.7492	-0.699	-0.4079	-0.1099	0.8275	0.6885	0.4918	0.5317	0.1732	0.0105	0.5208	0.1095	0.178	0.2561	-0.0443	0.3367	-28.5429	69.0745	-9.007
43	14.3288	-6.7333	1.7289	9.5093	7.3931	10.9828	-0.5012	0.2316	1.0844	0.4948	0.4352	-0.6835	0.0948	0.5713	0.0659	0.5613	0.1524	-0.077	0.3038	-0.0472	0.3871	-17.0361	72.9445	-8.9572
44	22.4085	-4.5167	-1.6952	2.134	-0.7136	1.1544	-0.3536	-0.7737	0.0082	0.8734	0.204	-0.3052	-0.6166	0.1284	0.1496	0.5585	0.1093	-0.2206	0.1847	-0.0517	0.2781	-13.288	64.9774	-12.706
45	15.1079	11.2938	3.0094	15.3334	-1.5274	4.762	0.1428	-0.4114	-0.4053	0.5237	-0.0285	0.7278	-0.0106	-0.0835	-0.1143	0.2779	0.036	0.1192	0.1779	0.0085	0.3405	-29.1547	58.0607	-17.7702
46	31.4455	4.9033	15.8665	9.4882	3.1244	19.2841	0.4249	0.4048	-0.8174	0.605	-0.1357	0.2583	0.9923	-0.1931	-0.2891	0.3393	0.0507	0.0978	0.158	-0.039	0.2574	-26.8492	50.4433	-18.2479
47	5.1463	0.0571	6.3008	10.1073	8.8373	21.0385	-0.0492	-0.1559	-0.5856	1.3034	0.5147	0.1898	0.8177	0.4235	-0.4655	0.6618	0.1647	0.0141	0.1542	0.0761	0.1861	-19.6401	52.8321	-11.2087
48	29.9855	1.3057	1.6925	34.3902	-2.3458	14.6925	0.6052	-1.166	0.0313	0.9586	0.1038	-0.6006	0.8473	0.1005	-0.7089	0.6586	0.1432	0.0092	0.5325	-0.0181	0.1829	-14.8995	57.229	-4.4584
49	9.657	0.2243	-2.2008	5.9803	1.1295	1.9986	-0.212	-1.0571	0.4388	1.0798	0.2601	-0.0829	0.2932	0.4142	-0.0481	0.4241	0.1175	-0.0008	0.2201	-0.0492	0.1331	-19.3564	63.3089	-11.5915
50	24.2417	9.3275	-8.022	6.3643	-7.1383	8.8427	0.1368	0.764	-0.0853	-0.1913	0.3229	0.4494	0.3135	-0.38	-0.4598	0.207	0.0287	0.0939	0.1379	0.0352	0.428	-36.308	61.5558	-23.7953
51	5.4144	-3.4944	3.6811	4.9966	0.4066	8.1928	-0.2555	-0.0622	0.0104	0.6334	0.0253	0.5112	0.5245	-0.3355	0.2303	0.4316	0.0338	0.3117	0.1799	0.0543	0.5483	-35.0141	58.3177	-10.4122
52	11.9435	-0.0398	5.7184	8.2012	-3.9107	4.7812	0.0075	-0.7911	0.0712	0.9317	-0.0233	0.0442	-0.197	-0.2176	0.0158	0.5492	0.1088	0.1246	0.2148	-0.0217	0.1481	-25.4886	62.5671	-8.5964
53	4.3816	2.3352	1.1395	15.9014	13.9649	16.7904	0.1509	0.4	1.6579	-0.54	-0.4949	0.8156	-0.9911	-0.7498	0.3439	0.9879	0.123	-0.0049	0.1738	0.1826	0.7628	-32.6069	72.6424	-22.0994
54	24.0085	4.5215	2.4687	7.859	-0.8663	14.9773	0.0305	0.7996	0.4726	-0.2665	0.0601	0.9819	0.2667	-0.7148	-0.0905	0.1251	0.0258	-0.0053	0.1903	0.0276	0.2284	-31.8379	68.9114	-26.0569
55	25.119	0.8572	3.4801	21.918	11.8566	12.7705	0.1752	0.8793	0.2334	-0.7234	0.2558	-0.0307	-0.2218	0.0506	-0.4311	0.1441	0.0051	0.0201	0.2404	0.0604	0.1161	-23.0637	68.5501	-27.0679
56	7.9885	1.614	1.959	7.9394	1.4519	1.3754	-0.2488	0.4484	0.07	0.0219	0.3163	-0.056	-0.0426	0.3394	-0.0676	0.2173	0.019	0.0103	0.2441	-0.0169	0.1188	-16.4925	62.4415	-20.3655
57	20.3348	6.3836	0.6469	9.0865	-1.5236	17.8547	-0.5679	0.4944	0.1661	0.0076	0.2564	-0.5012	-0.0088	1.1853	0.3115	0.1289	0.0126	-0.0361	0.2558	0.0896	0.2491	-10.7671	66.2932	-22.1566
58	24.3295	-3.2826	-1.4552	32.1058	-5.4316	6.9989	0.1598	0.3047	0.1375	-0.3372	-0.1246	-0.4847	0.0224	-0.1103	-0.0351	0.1745	-0.0079	-0.0244	0.2216	-0.0611	0.1297	-18.2061	52.5752	-23.821
59	15.8478	1.9914	2.2057	17.6344	1.3487	3.8359	-0.0101	0.1078	0.2976	0.0718	-0.0725	0.5225	-0.0978	-0.3064	0.0827	0.2	0.0711	-0.0726	0.1676	0.0079	0.1572	-9.1464	52.6822	-17.7462
60	24.4017	16.791	31.8942	12.2952	23.2292	44.1953	-1.1597	1.5737	0.0175	-0.8362	1.1929	-0.3193	-1.7759	2.2197	-0.0332	0.346	0.0243	-0.3647	0.2304	0.0015	1.1279	-2.1782	62.4697	-15.3869
61	3.8177	-0.1908	-0.1104	0.4582	0.9108	4.9742	-0.012	-0.1557	0.009	-0.0226	-0.3722	0.1635	-0.1953	0.004	0.3842	0.1848	0.0323	0.1033	0.4579	-0.0043	0.392	-54.4374	38.1381	-15.0827
62	3.9775	1.55	-0.5572	8.4714	-0.9227	0.1808	0.1366	0.3518	0.0208	-0.5215	-0.0923	0.584	0.0285	-0.1579	-0.0442	0.2656	-0.0292	-0.0427	0.4957	0.0257	0.5227	-52.8833	35.2201	-24.0811
63	1.5632	-3.7706	-1.5378	17.6917	2.4564	2.2163	-0.1826	-0.1132	0.0478	1.158	0.6483	1.1569	-0.0635	0.3901	-0.4657	0.1832	0.0507	0.2284	0.346	0.0056	0.3656	-43.9858	35.346	-15.9057
64	13.8998	-5.6553	-4.0998	11.3697	3.7108	1.9039	0.1895	-0.3707	0.4095	0.9125	-0.1166	0.2576	0.0621	-0.0692	-0.0729	0.4296	-0.0331	0.1683	0.202	-0.0351	0.2839	-35.1315	47.0141	-11.7093
65	6.0658	3.4654	1.9768	9.2542	3.9002	13.2107	0.2216	-0.0802	-0.1377	0.989	0.1367	-0.0618	0.0459	0.2983	-0.3582	0.19	0.0306	0.0396	0.1442	0.0301	0.1581	-33.839	37.5046	-17.6805
66	1.135	2.7907	-4.9365	31.529	-8.6419	24.7037	-0.0022	-0.1142	0.0382	-0.5681	0.2484	-0.7766	-0.4946	1.4762	-0.2461	0.1364	-0.0646	-0.0046	0.3836	-0.0438	0.2098	-37.2496	32.0117	-26.3566
67	10.6333	-4.2375	4.5211	13.8072	8.5275	20.5842	-0.045	0.6998	-0.0191	-0.758	0.3074	0.9254	-0.4429	-0.2519	-0.2624	0.1595	-0.051	-0.0242	0.285	0.0413	0.3629	-44.1874	28.2689	-25.4335
68	6.4028	-3.8633	-7.422	3.7543	6.5457	14.8203	-0.7781	-0.5259	-0.1204	0.5381	0.153	0.2131	0.3376	0.3085	0.6251	0.38	-0.023	0.1372	0.2646	0.029	0.4092	-45.5082	44.2522	-11.5798
69	1.8097	0.36	9.5902	13.274	9.0838	54.8668	-0.3914	0.0639	0.0568	-0.0175	-0.1884	0.5087	-1.8624	0.1447	0.5798	0.3805	-0.031	0.174	0.2839	0.0414	0.5456	-45.8655	55.0853	-10.7777
70	8.9334	-6.5324	-0.2791	8.3335	5.2324	8.7782	-0.0345	0.6593	0.1392	-0.0704	-0.3487	0.4829	-0.3256	0.069	0.3831	0.1733	-0.0171	0.1602	0.1605	0.048	0.5289	-40.0274	49.8238	-21.838
71	18.2884	-6.6788	-0.4134	10.4971	3.3598	1.3639	0.1827	0.7344	-0.7019	0.1452	-0.2518	0.5874	-0.0205	-0.0844	0.0691	0.1727	0.0585	0.089	0.1556	0.0699	0.3689	-45.232	41.7762	-21.7665
72	27.0153	16.3934	0.4739	13.0295	-1.5249	2.2745	0.7101	-0.2183	0.2212	0.2804	-0.1698	-0.015	-0.2027	-0.8836	-0.5402	0.2838	0.133	0.0338	0.7175	0.4674	0.9743	-55.4467	46.8504	-7.9074
73	8.5938	3.5743	5.5276	31.2189	6.9548	4.7281	-0.0502	-1.0207	0.1091	0.4327	0.0414	0.2636	-0.1713	-0.2644	0.0089	0.2599	0.0312	0.1078	0.5329	-0.0413	0.216	-52.8678	46.0779	-4.0774
74	0.5701	-2.4601	0.5843	15.5348	-3.6781	30.1667	-0.134	-0.111	0.1705	0.9706	-0.5301	0.0869	0.6431	0.2112	0.6641	0.211	-0.0737	0.0678	0.3938	-0.0874	0.2815	-50.9135	37.2347	-3.8655
75	4.8237	-1.2536	3.9078	3.8004	-2.5924	4.5192	-0.1706	-0.5989	0.109	0.4197	0.133	0.0167	-0.301	-0.3968	0.0376	0.53	-0.1711	0.2031	0.3906	-0.0263	0.1901	-42.1161	35.6244	-8.3461
76	6.8611	4.1922	0.8915	22.5373	3.5339	1.9305	-0.169	0.4586	-0.4181	0.8866	0.2354	1.4129	0.2544	-0.1113	-0.0665	0.3836	-0.1242	-0.016	0.309	0.0558	0.5162	-50.4823	22.2742	-16.2967
77	13.5875	20.1861	7.6206	32.8759	12.6442	16.7747	0.284	-0.2853	-0.199	1.2348	-0.2377	-0.8111	0.524	0.287	-0.0464	0.3123	0.0603	-0.0346	0.2855	0.0822	0.2734	-44.8302	27.3517	-8.3918
78	7.0191	-10.1475	-3.7738	24.5073	12.3377	11.2138	0.1321	-0.5311	0.6406	0.7632	-0.3603	-0.973	-0.3473	-0.0647	0.2282	0.6325	-0.1508	-0.0731	0.3312	0.1106	0.2759	-32.8393	34.1759	-8.895
79	28.9564	3.1876	6.0682	1.8294	1.303	1.6148	0.1773	-0.3035	-0.0937	0.3786	-0.0728	-0.0824	0.059	-0.0827	-0.1045	0.3463	-0.0266	0.059	0.1685	0.0045	0.129	-34.3005	24.9882	-14.098
80	7.9816	13.6446	11.943	36.8381	10.5771	26.6574	0.8974	-0.3248	-0.0557	1.5031	-0.5046	1.5281	1.7305	-0.5569	-0.3928	0.2137	0.0643	0.1813	0.255	0.0467	0.6931	-42.7614	18.2546	-17.4709

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 9
2	X-RAY DIFFRACTION	2	A	10 - 15
3	X-RAY DIFFRACTION	3	A	16 - 20
4	X-RAY DIFFRACTION	4	A	21 - 27
5	X-RAY DIFFRACTION	5	A	28 - 35
6	X-RAY DIFFRACTION	6	A	36 - 42
7	X-RAY DIFFRACTION	7	A	43 - 48
8	X-RAY DIFFRACTION	8	A	49 - 57
9	X-RAY DIFFRACTION	9	A	58 - 65
10	X-RAY DIFFRACTION	10	A	66 - 77
11	X-RAY DIFFRACTION	11	A	78 - 84
12	X-RAY DIFFRACTION	12	A	85 - 94
13	X-RAY DIFFRACTION	13	A	95 - 112
14	X-RAY DIFFRACTION	14	A	113 - 117
15	X-RAY DIFFRACTION	15	A	118 - 125
16	X-RAY DIFFRACTION	16	A	126 - 132
17	X-RAY DIFFRACTION	17	A	133 - 137
18	X-RAY DIFFRACTION	18	A	138 - 143
19	X-RAY DIFFRACTION	19	A	144 - 151
20	X-RAY DIFFRACTION	20	A	152 - 157
21	X-RAY DIFFRACTION	21	B	4 - 13
22	X-RAY DIFFRACTION	22	B	14 - 18
23	X-RAY DIFFRACTION	23	B	19 - 29
24	X-RAY DIFFRACTION	24	B	30 - 39
25	X-RAY DIFFRACTION	25	B	40 - 47
26	X-RAY DIFFRACTION	26	B	48 - 56
27	X-RAY DIFFRACTION	27	B	57 - 61
28	X-RAY DIFFRACTION	28	B	62 - 66
29	X-RAY DIFFRACTION	29	B	67 - 76
30	X-RAY DIFFRACTION	30	B	77 - 81
31	X-RAY DIFFRACTION	31	B	82 - 87
32	X-RAY DIFFRACTION	32	B	88 - 94
33	X-RAY DIFFRACTION	33	B	95 - 104
34	X-RAY DIFFRACTION	34	B	105 - 112
35	X-RAY DIFFRACTION	35	B	113 - 118
36	X-RAY DIFFRACTION	36	B	119 - 131
37	X-RAY DIFFRACTION	37	B	132 - 136
38	X-RAY DIFFRACTION	38	B	137 - 142
39	X-RAY DIFFRACTION	39	B	143 - 151
40	X-RAY DIFFRACTION	40	B	152 - 157
41	X-RAY DIFFRACTION	41	C	6 - 13
42	X-RAY DIFFRACTION	42	C	14 - 20
43	X-RAY DIFFRACTION	43	C	21 - 29
44	X-RAY DIFFRACTION	44	C	30 - 35
45	X-RAY DIFFRACTION	45	C	36 - 41
46	X-RAY DIFFRACTION	46	C	42 - 49
47	X-RAY DIFFRACTION	47	C	50 - 56
48	X-RAY DIFFRACTION	48	C	57 - 62
49	X-RAY DIFFRACTION	49	C	63 - 72
50	X-RAY DIFFRACTION	50	C	73 - 77
51	X-RAY DIFFRACTION	51	C	78 - 94
52	X-RAY DIFFRACTION	52	C	95 - 100
53	X-RAY DIFFRACTION	53	C	101 - 106
54	X-RAY DIFFRACTION	54	C	107 - 112
55	X-RAY DIFFRACTION	55	C	113 - 118
56	X-RAY DIFFRACTION	56	C	119 - 130
57	X-RAY DIFFRACTION	57	C	131 - 136
58	X-RAY DIFFRACTION	58	C	137 - 142
59	X-RAY DIFFRACTION	59	C	143 - 151
60	X-RAY DIFFRACTION	60	C	152 - 157
61	X-RAY DIFFRACTION	61	D	8 - 17
62	X-RAY DIFFRACTION	62	D	18 - 30
63	X-RAY DIFFRACTION	63	D	31 - 39
64	X-RAY DIFFRACTION	64	D	40 - 47
65	X-RAY DIFFRACTION	65	D	48 - 56
66	X-RAY DIFFRACTION	66	D	57 - 61
67	X-RAY DIFFRACTION	67	D	62 - 66
68	X-RAY DIFFRACTION	68	D	67 - 75
69	X-RAY DIFFRACTION	69	D	76 - 82
70	X-RAY DIFFRACTION	70	D	83 - 94
71	X-RAY DIFFRACTION	71	D	95 - 100
72	X-RAY DIFFRACTION	72	D	101 - 106
73	X-RAY DIFFRACTION	73	D	107 - 112
74	X-RAY DIFFRACTION	74	D	113 - 118
75	X-RAY DIFFRACTION	75	D	119 - 127
76	X-RAY DIFFRACTION	76	D	128 - 132
77	X-RAY DIFFRACTION	77	D	133 - 137
78	X-RAY DIFFRACTION	78	D	138 - 143
79	X-RAY DIFFRACTION	79	D	144 - 151
80	X-RAY DIFFRACTION	80	D	152 - 157

-
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