PDB-6amh: Engineered tryptophan synthase b-subunit from Pyrococcus furiosus...

ID or keywords:

Entry

Database: PDB / ID: 6amh

Title

Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB4D11 with Ser bound as E(Aex1)

Components

Tryptophan synthase beta chain 1

Keywords

BIOSYNTHETIC PROTEIN / PLP Type II /

Tryptophan Synthase /

Engineered /

Allostery

Function / homology

Function and homology information

tryptophan synthase /

tryptophan synthase activity
Similarity search - Function

Biological species

Pyrococcus furiosus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.63 Å

Authors

Buller, A.R.

Funding support

United States, 1items

Citation

Journal: J. Am. Chem. Soc. / Year: 2018
Title: Directed Evolution Mimics Allosteric Activation by Stepwise Tuning of the Conformational Ensemble.
Authors: Buller, A.R. / van Roye, P. / Cahn, J.K.B. / Scheele, R.A. / Herger, M. / Arnold, F.H.

History

Deposition	Aug 9, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 16, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 20, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Mar 23, 2022	Group: Author supporting evidence / Database references / Derived calculations Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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
Revision 1.3	Oct 4, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6amh.cif.gz	597.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6amh.ent.gz	495 KB	Display	PDB format
PDBx/mmJSON format	6amh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/am/6amh ftp://data.pdbj.org/pub/pdb/validation_reports/am/6amh	HTTPS FTP

-
Related structure data

Related structure data	5vm5C 6am7C 6am8C 6am9C 6amcC 6amiC 5dw0S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6cut-1 5vm5-2 6am7-2 6amc-1 6amc-2 6ami-3 1v8z-2 1v8z-1 6am7-1 5dvz-1 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (9)

Deposited unit

A: Tryptophan synthase beta chain 1

B: Tryptophan synthase beta chain 1

C: Tryptophan synthase beta chain 1

D: Tryptophan synthase beta chain 1

hetero molecules

175 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tryptophan synthase beta chain 1

B: Tryptophan synthase beta chain 1

hetero molecules

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

2

C: Tryptophan synthase beta chain 1

D: Tryptophan synthase beta chain 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	84.756, 109.600, 160.882
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Tryptophan synthase beta chain 1 Mass: 43466.695 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea) Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: trpB1, PF1706 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U093, tryptophan synthase
#2: Chemical	ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE Mass: 336.235 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₇N₂O₈P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.15 Å³/Da / Density % sol: 42.76 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 15-25% PEG3350 and 0.1 M Na HEPES pH 7.85

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.63→40 Å / Num. obs: 186378 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC_1/2: 0.999 / R_pim(I) all: 0.035 / Net I/σ(I): 12.2
Reflection shell	Resolution: 1.63→1.66 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 9142 / CC_1/2: 0.327 / R_pim(I) all: 1.191 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5DW0

5dw0

Resolution: 1.63→40 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.956 / SU B: 6.495 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2328	9239	5 %	RANDOM
R_work	0.20651	-	-	-
obs	0.20782	175962	99.21 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 33.403 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.68 Å²	0 Å²	0 Å²
2-	-	1.86 Å²	-0 Å²
3-	-	-	-2.54 Å²

Refinement step

Cycle: 1 / Resolution: 1.63→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11681	0	92	577	12350

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.019	12048
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	11215
X-RAY DIFFRACTION	r_angle_refined_deg	1.154	1.969	16322
X-RAY DIFFRACTION	r_angle_other_deg	0.88	3	25901
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.533	5	1550
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.436	23.956	498
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.554	15	1947
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.272	15	61
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	1793
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	13621
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2428
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	0.296	1.487	6218
X-RAY DIFFRACTION	r_mcbond_other	0.296	1.487	6217
X-RAY DIFFRACTION	r_mcangle_it	0.555	2.227	7762
X-RAY DIFFRACTION	r_mcangle_other	0.555	2.227	7763
X-RAY DIFFRACTION	r_scbond_it	0.18	1.54	5830
X-RAY DIFFRACTION	r_scbond_other	0.18	1.54	5830
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.355	2.297	8561
X-RAY DIFFRACTION	r_long_range_B_refined	3.788	17.958	13277
X-RAY DIFFRACTION	r_long_range_B_other	3.725	17.721	13194
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.63→1.672 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.391	639	-
R_work	0.373	12215	-
obs	-	-	94.24 %

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	1.4933	-0.2528	-1.2052	2.7069	1.7247	3.89	-0.1535	-0.3346	-0.0186	0.3882	0.1241	-0.1311	0.6393	0.5146	0.0294	0.2144	0.121	-0.0725	0.2234	0.0546	0.1174	9.6215	-49.1022	0.6988
2	0.8107	-0.1114	-0.3418	1.2159	0.0488	1.6164	0.0351	-0.0459	0.0874	-0.0741	-0.0393	-0.1054	0.1098	0.2185	0.0042	0.1219	0.0407	0.0017	0.1408	0.0188	0.2699	8.9686	-40.1298	-20.9467
3	2.0481	-0.9618	-1.8551	1.6779	0.9421	3.625	-0.1111	-0.021	0.0342	0.0476	-0.0326	-0.038	0.3848	-0.0436	0.1437	0.1978	-0.0118	0.0009	0.1091	0.014	0.2207	-2.4477	-50.6486	-17.7767
4	1.8737	-0.5305	-2.3463	2.5574	1.1498	5.1417	-0.1033	0.1046	0.0651	0.1133	-0.0713	0.2423	0.0828	-0.6087	0.1746	0.1265	-0.0321	-0.0069	0.2264	-0.0345	0.1797	-12.0284	-47.2521	-15.9622
5	0.7407	-0.3052	0.0223	1.6471	-0.0264	1.7584	-0.0552	-0.2333	0.0256	0.2036	0.0267	-0.0663	0.3679	0.1643	0.0285	0.1814	0.0629	-0.0225	0.1673	0.0183	0.2074	6.2423	-45.9947	-8.8866
6	2.3249	-0.8057	-0.3855	1.1184	-0.2157	1.9767	-0.032	-0.2217	0.3261	0.0632	0.0517	-0.3439	-0.3004	0.4491	-0.0197	0.0986	-0.0552	-0.0315	0.1309	-0.047	0.2889	11.1555	-26.963	-11.8173
7	3.1085	-3.6891	1.786	5.4467	-3.039	4.2346	-0.1016	-0.29	0.0725	0.3689	0.1635	0.143	-0.3177	-0.2867	-0.0619	0.1722	0.0317	0.008	0.1937	-0.0298	0.1667	-5.6525	-31.8988	0.3026
8	0.4035	-0.3955	-0.6633	9.1591	-12.4182	21.0626	-0.2914	0.0107	0.0977	0.5058	0.2434	-0.194	0.2257	-0.9214	0.048	0.2586	-0.0377	0.0047	0.6135	0.0252	0.1812	-11.7957	-35.4321	3.17
9	1.523	-0.3293	0.0906	0.8879	-0.282	3.1566	0.0821	-0.2085	0.206	0.071	-0.0031	-0.0856	-0.2192	-0.1017	-0.0791	0.1367	0.0326	0.007	0.0667	-0.0266	0.2493	-1.6111	-26.9629	-12.9068
10	3.3982	-0.4361	0.9936	1.4354	-0.3602	1.852	0.1031	-0.087	0.3617	-0.0519	-0.0693	-0.1374	-0.2674	-0.0176	-0.0339	0.1807	0.0495	0.0553	0.1405	-0.0094	0.2399	-1.7433	-24.0796	-21.3225
11	1.1513	0.4913	0.7776	1.8575	0.4939	3.0077	-0.0344	0.2357	0.2198	-0.4549	0.0166	-0.2172	-0.4552	0.2568	0.0177	0.2269	0.0587	0.1429	0.1386	0.1327	0.1851	8.875	-25.2095	-54.962
12	0.3168	-0.2753	-0.0859	0.9831	0.3509	1.5266	0.0369	0.0885	0.0386	-0.1075	-0.0689	-0.093	-0.109	-0.0705	0.032	0.1816	0.0599	0.0482	0.1078	0.0504	0.2536	3.504	-34.9778	-39.6506
13	3.4181	2.2471	1.2648	8.1272	4.8992	6.1195	0.0064	0.2635	-0.2061	0.1441	-0.2347	0.3526	0.2761	-0.701	0.2283	0.1623	0.0779	0.027	0.2589	0.0033	0.1846	-12.7268	-31.8759	-36.954
14	0.3067	-0.253	0.0448	1.3547	-0.0277	1.7644	0.0889	0.1116	0.0708	-0.3519	-0.1225	-0.0204	-0.1857	-0.1712	0.0336	0.2231	0.0967	0.0438	0.1077	0.0437	0.1759	1.6064	-32.876	-49.6094
15	3.4061	1.0238	-0.5798	1.9892	0.0624	2.2948	0.0271	0.257	-0.0275	-0.3019	-0.044	-0.1875	0.2357	-0.027	0.0168	0.2699	0.1044	0.0537	0.1441	0.0275	0.1684	7.5672	-46.8882	-50.7964
16	5.1404	1.5044	-1.1036	2.5373	-1.9945	2.1332	-0.0316	0.339	-0.2236	-0.3629	-0.0559	-0.0779	0.3761	-0.3913	0.0875	0.3038	0.0414	0.0113	0.4088	-0.0378	0.0117	-6.4555	-44.9246	-60.1225
17	2.7555	-3.4124	5.0683	12.4328	-4.5114	9.9623	-0.0692	-0.2649	0.1205	-0.4213	-0.3054	-0.1093	-0.3404	-0.9978	0.3747	0.2338	0.0161	-0.1408	0.838	-0.0804	0.2207	-13.4939	-43.2824	-58.2456
18	1.1291	-0.381	-0.2158	0.8041	0.0607	1.8803	0.0414	0.2301	-0.0998	-0.2018	-0.1114	0.014	0.2948	-0.296	0.0699	0.255	0.0397	0.0163	0.1102	-0.0121	0.163	-0.9962	-49.5676	-46.5768
19	3.2366	-0.8151	-0.9281	2.4458	0.1085	1.7957	0.0104	0.1221	-0.1379	-0.053	-0.086	-0.0316	0.3277	-0.2024	0.0757	0.265	-0.004	0.0069	0.1242	-0.0036	0.1337	2.1378	-52.9805	-39.4276
20	0.0565	-0.01	-0.5585	0.0037	0.0509	9.2607	-0.1042	-0.0059	0.0101	0.0298	-0.0216	0.0017	0.4184	0.1277	0.1257	0.3013	-0.069	-0.0786	0.374	0.0039	0.5509	-16.471	-60.7965	-31.2152
21	1.6049	-0.4499	0.7492	1.166	-0.5296	3.4148	-0.0989	-0.4156	0.025	0.1949	0.2482	0.24	-0.1053	-0.64	-0.1493	0.0345	0.0656	0.0431	0.3878	0.0859	0.1433	27.5758	-11.1383	-26.7061
22	0.6815	-0.1176	0.289	0.7711	-0.5077	1.1595	0.048	-0.0043	-0.0101	-0.1285	0.0576	-0.0079	0.08	-0.3119	-0.1057	0.1192	-0.0405	-0.0171	0.1666	0.0405	0.2438	37.6754	-18.9114	-41.5455
23	2.7089	-0.5412	1.2628	1.6704	-0.4734	4.044	-0.1323	-0.0916	0.0158	0.1089	0.0637	-0.1415	-0.3053	0.1724	0.0686	0.1652	-0.0077	0.0043	0.0933	0.0077	0.2228	46.8586	-3.3496	-35.6765
24	0.949	-0.481	-0.1329	1.5853	-0.0418	1.6553	-0.0305	-0.2688	0.0124	0.1233	0.1217	0.0671	-0.1513	-0.4881	-0.0912	0.0994	0.0314	0.013	0.258	0.0497	0.1979	33.7344	-12.5471	-29.7641
25	2.647	0.3373	-0.0737	0.8534	0.512	1.9836	0.0208	-0.2163	-0.2634	-0.038	0.0323	0.1542	0.3858	-0.4252	-0.0531	0.1978	-0.1054	-0.0217	0.1599	0.1069	0.2295	37.5187	-31.0827	-32.9036
26	7.3705	-3.888	-2.7094	2.1239	1.8131	3.6605	-0.0791	-0.4371	0.0116	0.0807	0.1654	-0.0409	0.1737	0.0466	-0.0863	0.1871	0.0118	-0.0146	0.2114	0.0092	0.1878	50.8995	-20.6238	-20.0147
27	2.5426	-3.5772	-4.8562	11.5555	8.598	9.7902	0.1662	-0.5454	0.0698	0.9022	0.0128	-0.0556	-0.0299	0.9131	-0.179	0.3411	-0.1354	-0.0466	0.5354	-0.1135	0.1901	55.4688	-14.9643	-17.3645
28	1.5029	-0.0482	0.1529	0.6329	-0.1964	2.4337	0.0631	-0.1535	-0.0852	0.0024	0.0514	-0.0142	0.2762	0.1426	-0.1145	0.1748	0.0183	-0.0234	0.0679	0.0301	0.213	49.3143	-25.8736	-33.7086
29	6.4087	-1.0381	-1.7794	4.7569	1.174	3.9732	-0.265	-0.3825	-0.6597	0.0263	0.1671	-0.0927	0.6353	0.3716	0.0979	0.336	-0.0169	-0.0507	0.0676	0.0523	0.1962	45.1049	-40.576	-38.5808
30	7.072	1.0721	-1.0689	2.961	-0.6131	2.6774	0.1313	0.0842	0.18	-0.0792	-0.0681	-0.3798	-0.134	0.4207	-0.0632	0.2551	0.007	-0.0032	0.2123	-0.0006	0.2106	53.5358	-18.128	-44.1244
31	1.2487	0.3059	-0.004	2.7699	-2.2659	3.3922	-0.0304	0.2675	-0.2188	-0.5249	0.0289	0.0508	0.7283	-0.1548	0.0015	0.3829	-0.0922	-0.0576	0.1238	-0.0721	0.0908	41.4381	-29.4702	-77.975
32	0.7746	-0.2284	-0.0226	1.119	-0.1533	1.3844	-0.0245	0.1007	0	-0.0938	0.081	0.0482	0.2239	-0.236	-0.0565	0.202	-0.0528	-0.0603	0.1588	0.0219	0.1972	38.1454	-18.8235	-59.5254
33	1.974	0.8121	-0.6975	3.6794	-1.6334	2.586	-0.1095	0.0966	0.0917	-0.0452	-0.0517	-0.0643	0.0028	0.3054	0.1612	0.2318	0.0209	-0.0399	0.2022	-0.0211	0.1334	55.3708	-20.85	-59.9749
34	1.6629	0.2362	0.0739	4.0744	-0.0117	1.531	-0.0216	0.2851	-0.0001	-0.4776	-0.2562	-0.4105	0.2288	0.4317	0.2778	0.2774	0.0677	0.05	0.2707	0.0519	0.1408	58.7458	-23.3504	-72.601
35	0.1523	-0.1284	-0.4359	0.9387	0.4232	2.1925	-0.0501	0.143	-0.0114	-0.2193	0.1127	0.1207	0.4736	-0.2746	-0.0626	0.2407	-0.0853	-0.069	0.2165	0.0116	0.1551	37.0278	-20.9197	-70.0912
36	1.5949	0.1846	-0.0996	1.2111	-0.1417	2.3442	-0.0236	0.1672	0.0413	-0.1515	0.072	0.0652	-0.0288	-0.3178	-0.0483	0.1526	-0.039	-0.0694	0.2213	0.0563	0.1832	33.9658	-7.4379	-70.0402
37	2.1181	0.2064	0.4566	3.3008	0.328	4.3859	-0.0504	0.1943	0.2855	-0.4442	0.1808	-0.2244	-0.1175	0.5789	-0.1304	0.2201	-0.0948	-0.0065	0.2771	0.0224	0.0902	50.2093	-7.779	-82.7672
38	1.0538	-0.1234	0.0586	0.5496	0.0038	3.1576	-0.0503	0.1495	0.1365	-0.1168	0.1306	0.0419	-0.1343	-0.0086	-0.0803	0.1588	-0.0369	-0.0312	0.125	0.0614	0.2145	41.4035	-3.7957	-66.7772
39	3.5287	-1.0504	1.5241	2.072	0.0719	1.3127	-0.1123	0.0759	0.2727	-0.0021	0.0478	0.2446	-0.2243	-0.2407	0.0645	0.1525	0.0272	-0.0198	0.2629	0.1135	0.1901	30.058	-1.7774	-61.8806
40	7.6598	4.516	1.8453	11.3989	-0.0014	5.7322	-0.0921	-0.0399	0.4652	0.0815	0.0874	-0.2341	-0.4946	0.7198	0.0047	0.2171	0.0022	-0.0307	0.2874	-0.0089	0.2136	52.3186	-3.2801	-53.847

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 31
2	X-RAY DIFFRACTION	2	A	32 - 107
3	X-RAY DIFFRACTION	3	A	108 - 132
4	X-RAY DIFFRACTION	4	A	133 - 164
5	X-RAY DIFFRACTION	5	A	165 - 212
6	X-RAY DIFFRACTION	6	A	213 - 254
7	X-RAY DIFFRACTION	7	A	255 - 281
8	X-RAY DIFFRACTION	8	A	282 - 292
9	X-RAY DIFFRACTION	9	A	293 - 353
10	X-RAY DIFFRACTION	10	A	354 - 388
11	X-RAY DIFFRACTION	11	B	1 - 42
12	X-RAY DIFFRACTION	12	B	43 - 132
13	X-RAY DIFFRACTION	13	B	133 - 147
14	X-RAY DIFFRACTION	14	B	148 - 223
15	X-RAY DIFFRACTION	15	B	224 - 255
16	X-RAY DIFFRACTION	16	B	256 - 281
17	X-RAY DIFFRACTION	17	B	282 - 293
18	X-RAY DIFFRACTION	18	B	294 - 352
19	X-RAY DIFFRACTION	19	B	353 - 383
20	X-RAY DIFFRACTION	20	B	384 - 394
21	X-RAY DIFFRACTION	21	C	1 - 44
22	X-RAY DIFFRACTION	22	C	45 - 108
23	X-RAY DIFFRACTION	23	C	109 - 167
24	X-RAY DIFFRACTION	24	C	168 - 212
25	X-RAY DIFFRACTION	25	C	213 - 254
26	X-RAY DIFFRACTION	26	C	255 - 281
27	X-RAY DIFFRACTION	27	C	282 - 292
28	X-RAY DIFFRACTION	28	C	293 - 352
29	X-RAY DIFFRACTION	29	C	353 - 368
30	X-RAY DIFFRACTION	30	C	369 - 385
31	X-RAY DIFFRACTION	31	D	1 - 39
32	X-RAY DIFFRACTION	32	D	40 - 107
33	X-RAY DIFFRACTION	33	D	108 - 148
34	X-RAY DIFFRACTION	34	D	149 - 180
35	X-RAY DIFFRACTION	35	D	181 - 212
36	X-RAY DIFFRACTION	36	D	213 - 265
37	X-RAY DIFFRACTION	37	D	266 - 290
38	X-RAY DIFFRACTION	38	D	291 - 352
39	X-RAY DIFFRACTION	39	D	353 - 374
40	X-RAY DIFFRACTION	40	D	375 - 385

-
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