PDB-6am9: Engineered tryptophan synthase b-subunit from Pyrococcus furiosus...

ID or keywords:

Entry

Database: PDB / ID: 6am9

Title

Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9, with Ser-bound in a predominantly closed state.

Components

Tryptophan synthase beta chain 1

Keywords

LYASE / PLP Type II / Tryptophan Synthase / Engineered / Allostery / BIOSYNTHETIC PROTEIN

Function / homology

Function and homology information

tryptophan synthase / tryptophan synthase activity / cytoplasm
Similarity search - Function

Biological species

Pyrococcus furiosus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.09 Å

Authors

Buller, A.R. / van Roye, P.

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	Oct 4, 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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6am9.cif.gz	583.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6am9.ent.gz	486.9 KB	Display	PDB format
PDBx/mmJSON format	6am9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6am9_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	6am9_full_validation.pdf.gz	1.7 MB	Display
Data in XML	6am9_validation.xml.gz	51.1 KB	Display
Data in CIF	6am9_validation.cif.gz	70.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/am/6am9 ftp://data.pdbj.org/pub/pdb/validation_reports/am/6am9	HTTPS FTP

-
Related structure data

Related structure data	5vm5SC 6am7C 6am8C 6amcC 6amhC 6amiC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6cuv-1 5dw3-1 5dw0-1 6ami-1 5vm5-1 5t6m-2 6am7-1 6am8-1 6cuv-2 5t6m-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
87.5 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
87.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.502, 109.122, 160.491
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: 43390.602 Da / Num. of mol.: 4 Mutation: I16V, E17G, I68V, F95L, F274S, T292S, T321A, V384A 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 BL21(DE3) (bacteria) / References: UniProt: Q8U093, tryptophan synthase
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE Mass: 336.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₇N₂O₈P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid Mass: 316.204 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₁H₁₃N₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.21 Å³/Da / Density % sol: 44.28 %
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: Aug 3, 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: 2.09→40 Å / Num. obs: 91166 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC_1/2: 0.998 / R_pim(I) all: 0.03 / Net I/σ(I): 13.5
Reflection shell	Resolution: 2.09→2.13 Å / Redundancy: 6.9 % / Num. unique obs: 30761 / CC_1/2: 0.695 / R_pim(I) all: 0.739 / % possible all: 99.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5VM5

5vm5

Resolution: 2.09→40 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.949 / SU B: 20.665 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24397	4524	5 %	RANDOM
R_work	0.21449	-	-	-
obs	0.216	86509	99.42 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 60.15 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.91 Å²	0 Å²	-0 Å²
2-	-	-2.34 Å²	0 Å²
3-	-	-	-0.57 Å²

Refinement step

Cycle: 1 / Resolution: 2.09→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11369	0	91	106	11566

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	11731
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	11114
X-RAY DIFFRACTION	r_angle_refined_deg	1.21	1.958	15921
X-RAY DIFFRACTION	r_angle_other_deg	0.898	2.996	25424
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.722	5	1538
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.916	23.922	459
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.183	15	1815
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.383	15	54
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	1774
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	13509
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2641
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	0.443	2.358	6162
X-RAY DIFFRACTION	r_mcbond_other	0.441	2.358	6161
X-RAY DIFFRACTION	r_mcangle_it	0.778	3.532	7690
X-RAY DIFFRACTION	r_mcangle_other	0.778	3.532	7691
X-RAY DIFFRACTION	r_scbond_it	0.345	2.41	5569
X-RAY DIFFRACTION	r_scbond_other	0.342	2.41	5569
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.611	3.609	8229
X-RAY DIFFRACTION	r_long_range_B_refined	4.179	19.168	13007
X-RAY DIFFRACTION	r_long_range_B_other	4.176	19.154	13000
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.09→2.144 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.397	318	-
R_work	0.414	6298	-
obs	-	-	99.07 %

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	3.7651	-1.9677	-1.4966	4.7227	0.5074	1.497	-0.3273	-0.5408	-0.3405	0.9787	0.0851	-0.4571	0.4189	0.5223	0.2422	0.5976	0.0673	-0.1246	0.6626	0.1498	0.1531	9.215	-50.402	-2.711
2	1.0172	0.0313	0.529	5.234	-0.2072	3.1989	0.0532	-0.1379	0.0242	-0.0723	-0.0577	-0.1682	-0.4164	0.2578	0.0045	0.3584	-0.1025	-0.0571	0.5583	0.0025	0.1727	7.805	-34.688	-23.465
3	7.1879	-1.8213	3.0478	9.6892	4.3467	4.3785	0.2678	-0.1128	-0.5923	0.6153	0.4014	-0.5895	0.7731	0.307	-0.6692	0.6096	0.0426	-0.0959	0.4725	0.14	0.2256	3.793	-58.755	-12.358
4	2.5164	-0.7703	-0.4835	5.1371	3.0972	5.9653	0.0248	-0.1954	-0.1875	0.0889	-0.3376	0.308	0.0315	-0.1905	0.3127	0.4316	-0.0939	-0.0618	0.4981	0.0515	0.169	-6.086	-49.114	-17.258
5	3.2759	0.3846	-1.8369	2.0046	2.6667	10.7684	-0.0787	-0.2147	-0.083	0.1945	-0.3993	0.5492	-0.275	-0.9194	0.478	0.4251	-0.0686	-0.0036	0.4962	-0.0104	0.2445	-12.335	-48.207	-14.884
6	1.0483	0.0056	-0.0032	1.9726	0.3984	2.8131	0.1129	-0.479	-0.1306	0.4461	-0.0875	-0.3021	-0.1283	0.2922	-0.0253	0.457	-0.108	-0.1134	0.6332	0.0392	0.0692	7.855	-37.611	-10.268
7	4.7937	-4.6209	0.6201	6.4151	-4.1329	7.3802	-0.0093	-0.2897	-0.1241	0.3578	0.0355	0.2582	-0.5235	-0.2734	-0.0262	0.5997	-0.0413	-0.0022	0.6579	-0.1421	0.1047	-7.179	-31.983	-0.01
8	2.4515	1.5482	-2.8258	1.2285	-1.8451	11.0353	0.5289	-0.3186	-0.3088	0.4561	-0.0835	0.1065	0.1938	-0.6257	-0.4455	0.6303	-0.0587	0.0616	0.6625	0.0963	0.5533	-12.015	-34.627	-3.996
9	0.917	-0.0892	0.4677	1.3777	0.0769	4.3464	0.0479	-0.2634	0.1817	0.0847	-0.0828	-0.0632	-0.8881	-0.0952	0.0349	0.5667	-0.032	-0.0501	0.491	-0.0909	0.0559	1.127	-24.717	-14.854
10	6.1171	-5.3249	0.5955	14.2492	2.2387	7.9658	-0.1167	-0.0727	-0.0768	-0.4915	0.0013	0.7682	-0.5572	-1.111	0.1154	0.477	0.0718	-0.1084	0.5721	-0.0603	0.2267	-13.688	-31.717	-24.892
11	0.7591	0.2455	0.8516	2.0286	-0.7293	4.3319	-0.2396	0.1735	0.1193	-0.2326	-0.0581	-0.232	-1.0027	0.8095	0.2977	0.5206	-0.2482	0.0004	0.5655	0.0465	0.0593	9.919	-27.144	-53.701
12	0.1695	0.5062	0.3314	1.7496	1.7074	3.9791	-0.0183	0.0366	-0.1172	0.0415	0.0409	-0.2109	0.2901	0.2836	-0.0226	0.3463	-0.0246	-0.0133	0.5589	-0.0045	0.2625	7.497	-46.843	-35.37
13	2.136	-0.1376	-2.2614	3.0128	1.1599	5.7896	-0.2794	0.0426	0.1098	0.1365	-0.0624	0.1174	-0.3724	0.0556	0.3418	0.649	-0.0845	-0.1119	0.4258	0.0045	0.0677	-1.705	-25.596	-43.876
14	5.7376	-5.4702	-4.3949	5.2503	4.1731	3.3757	-0.1586	0.4007	-0.835	0.3081	-0.424	0.8603	0.048	-0.2954	0.5826	0.8982	-0.2543	0.1259	0.6414	0.0032	0.5468	-14.081	-37.597	-39.774
15	2.0032	-0.6627	-2.7598	4.801	0.5944	7.5856	-0.2021	0.4539	-0.1551	-0.4093	-0.4781	0.5235	-0.2086	-1.1247	0.6802	0.5091	-0.0095	-0.1534	0.5483	-0.1274	0.1339	-10.474	-26.821	-47.748
16	0.8023	-0.3662	0.949	2.8946	-0.833	3.5235	-0.0294	0.1884	-0.1432	-0.2398	0.0146	-0.2359	-0.2237	0.6905	0.0148	0.38	-0.094	0.0456	0.6254	-0.0087	0.1231	9.531	-40.38	-47.535
17	0.6915	0.3821	0.1098	1.3068	-0.4347	3.7738	-0.1344	0.1075	-0.0564	-0.5499	0.0874	-0.1102	0.1888	0.0438	0.047	0.468	-0.0513	0.0246	0.5207	-0.0805	0.0793	1.331	-47.484	-55.611
18	2.1285	-0.4404	0.7743	0.3255	0.5833	2.698	-0.0827	0.1638	0.0942	-0.1348	-0.1266	0.0868	-0.4828	-0.2387	0.2093	0.6172	-0.0555	-0.0891	0.889	0.1356	0.5236	-11.709	-43.75	-61.647
19	1.2726	0.3881	-0.1178	1.2088	0.3131	5.1348	-0.0267	0.1767	-0.1337	-0.2493	-0.0053	-0.0034	0.4077	-0.1546	0.032	0.3728	-0.0408	-0.0269	0.4779	-0.0555	0.177	-1.537	-50.358	-46.581
20	1.6958	-0.1884	0.4361	1.8896	0.0476	4.2604	-0.0373	0.1377	-0.19	-0.0696	-0.0543	0.0277	0.7545	0.0025	0.0916	0.4558	-0.089	-0.015	0.4928	-0.0455	0.185	-0.103	-53.518	-39.418
21	3.8503	-0.8437	0.1405	3.1442	0.7196	0.9893	0.0514	-0.4895	0.1955	1.3288	-0.1122	0.3136	0.5697	-0.4059	0.0608	0.9076	-0.199	0.0896	0.7023	0.056	0.0893	29.969	-14.14	-18.869
22	1.2966	0.1659	0.3671	1.2871	-0.5587	2.2092	0.1769	0.0083	0.0099	-0.0696	0.0377	0.106	0.3308	-0.2773	-0.2146	0.5252	-0.0731	-0.0434	0.5174	0.0339	0.0821	33.22	-20.117	-42.195
23	2.6438	0.3139	0.6068	3.299	-0.2848	5.5173	0.1486	0.0898	-0.0161	0.2329	-0.3348	-0.4344	0.2412	0.7264	0.1861	0.4081	-0.0134	-0.0289	0.4871	0.0721	0.2065	45.699	-8.702	-37.344
24	2.816	0.284	0.4802	3.8913	0.2799	5.9063	0.0435	-0.3266	0.1134	1.0046	-0.2358	-0.477	0.0999	0.6793	0.1922	0.5313	-0.0606	-0.1248	0.4247	0.0453	0.1342	46.297	-5.698	-29.044
25	0.852	0.7056	-0.0815	4.1371	1.3678	0.9541	0.2472	-0.3089	-0.1212	0.2408	-0.285	0.0795	0.1706	-0.2682	0.0378	0.568	-0.1318	-0.0347	0.5142	0.0748	0.0895	32.072	-19.877	-31.891
26	4.0525	0.8091	-0.049	2.4445	0.8591	0.7913	0.0259	-0.1594	-0.3231	0.3761	-0.0079	0.2994	0.4069	-0.0084	-0.0181	0.749	-0.059	-0.1056	0.3727	0.0943	0.1591	36.236	-33.763	-34.297
27	12.7621	-6.5488	-5.8663	4.0368	1.7765	5.3936	-0.4263	-0.1988	-0.6509	0.3964	-0.0566	0.1347	0.4107	0.2636	0.4829	0.8576	-0.0626	-0.2521	0.4752	0.0536	0.1689	49.62	-26.054	-20.125
28	4.6703	-2.2416	-0.5711	1.399	-0.9717	4.9028	0.0987	-0.54	-0.0576	-0.2023	0.1031	0.0731	0.7273	0.6074	-0.2019	0.9923	-0.0051	-0.1923	0.4156	0.0104	0.039	49.777	-22.637	-21.625
29	1.6916	0.1116	-0.5483	2.1627	0.4533	2.1633	0.2524	-0.0407	-0.4474	0.2577	-0.2051	-0.2389	0.5569	0.2755	-0.0472	0.7744	0.112	-0.1931	0.3651	0.0397	0.1609	46.579	-33.382	-36.388
30	2.5058	-0.5943	0.6998	3.0467	0.9332	0.9286	0.1474	0.0629	-0.1701	-0.0572	-0.0585	-0.2218	0.4308	0.1477	-0.0889	0.6723	0.1261	-0.0806	0.492	0.033	0.1765	46.69	-29.486	-42.771
31	2.7075	-1.5981	0.5688	8.7527	1.6565	1.281	0.1998	0.1533	-0.2206	-0.471	-0.1386	-0.2948	0.4542	0.3491	-0.0613	0.6724	0.1402	0.058	0.5823	0.0301	0.0987	46.793	-20.494	-86.15
32	3.5974	-1.0458	-3.6363	2.6357	0.8158	7.6648	-0.0208	0.2286	-0.6051	-0.2453	-0.1108	0.3108	1.1445	-0.3074	0.1317	0.7799	0.0018	-0.1672	0.3	-0.0407	0.1661	37.249	-33.744	-70.167
33	1.1351	-1.4817	0.749	4.4788	-0.3384	2.7611	-0.015	0.053	0.1853	0.197	0.0253	0.1103	0.1861	-0.2621	-0.0103	0.3878	-0.01	-0.0146	0.4844	0.0091	0.1884	33.598	-11.568	-55.453
34	0.6156	-0.2083	1.4479	5.0882	-1.3008	4.2252	-0.0708	0.229	-0.0288	0.0522	0.1499	0.0354	0.4323	0.4604	-0.0791	0.734	0.1886	-0.0477	0.4234	-0.0569	0.0157	48.345	-28.31	-65.178
35	3.073	0.4746	0.9792	3.076	-1.418	4.9446	-0.1938	0.3374	0.1769	0.1493	-0.2224	-0.436	0.2463	2.0962	0.4162	0.4708	0.1921	-0.0436	1.0313	0.1389	0.0924	58.281	-22.107	-65.476
36	0.4509	-0.0256	1.0102	0.8007	-0.3153	2.3975	0.2185	0.088	-0.0857	-0.3405	-0.008	0.0847	0.7598	0.1537	-0.2105	0.7492	0.056	-0.0332	0.4948	-0.0144	0.0278	38.559	-21.294	-70.596
37	1.0407	-0.04	0.6352	1.3803	0.5012	3.3203	-0.0521	0.2596	0.0482	-0.2929	0.0932	0.1078	-0.0138	-0.1071	-0.0411	0.4661	0.0312	-0.0056	0.5081	0.0597	0.18	35.181	-7.201	-69.406
38	1.1638	0.3414	2.7896	4.2802	2.3545	7.3077	-0.0155	0.4403	0.0396	-0.789	0.2391	-0.7414	-0.399	1.1699	-0.2236	0.4083	0.0012	0.1826	0.6504	0.0653	0.2307	52.12	-6.809	-77.346
39	0.8923	0.0094	0.3449	0.9431	-0.0007	4.1445	0.0452	0.1175	0.1937	-0.1949	-0.0486	0.0038	-0.1781	-0.0218	0.0034	0.3687	0.0065	0.0038	0.437	0.0567	0.2147	38.225	-3.41	-63.895
40	9.0605	4.0489	-0.271	16.5533	-2.7641	3.675	0.0809	-0.1634	0.4843	0.7493	-0.159	-0.3434	-0.662	0.8374	0.0781	0.4436	0.0068	-0.0407	0.5262	-0.0135	0.2539	52.756	-4.776	-52.368

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 39
2	X-RAY DIFFRACTION	2	A	40 - 91
3	X-RAY DIFFRACTION	3	A	92 - 102
4	X-RAY DIFFRACTION	4	A	103 - 136
5	X-RAY DIFFRACTION	5	A	137 - 169
6	X-RAY DIFFRACTION	6	A	170 - 254
7	X-RAY DIFFRACTION	7	A	255 - 281
8	X-RAY DIFFRACTION	8	A	282 - 301
9	X-RAY DIFFRACTION	9	A	302 - 374
10	X-RAY DIFFRACTION	10	A	375 - 385
11	X-RAY DIFFRACTION	11	B	1 - 44
12	X-RAY DIFFRACTION	12	B	45 - 85
13	X-RAY DIFFRACTION	13	B	86 - 132
14	X-RAY DIFFRACTION	14	B	133 - 140
15	X-RAY DIFFRACTION	15	B	141 - 178
16	X-RAY DIFFRACTION	16	B	179 - 232
17	X-RAY DIFFRACTION	17	B	233 - 280
18	X-RAY DIFFRACTION	18	B	281 - 292
19	X-RAY DIFFRACTION	19	B	293 - 351
20	X-RAY DIFFRACTION	20	B	352 - 385
21	X-RAY DIFFRACTION	21	C	1 - 29
22	X-RAY DIFFRACTION	22	C	30 - 102
23	X-RAY DIFFRACTION	23	C	103 - 142
24	X-RAY DIFFRACTION	24	C	143 - 178
25	X-RAY DIFFRACTION	25	C	179 - 211
26	X-RAY DIFFRACTION	26	C	212 - 257
27	X-RAY DIFFRACTION	27	C	258 - 276
28	X-RAY DIFFRACTION	28	C	277 - 306
29	X-RAY DIFFRACTION	29	C	307 - 359
30	X-RAY DIFFRACTION	30	C	360 - 383
31	X-RAY DIFFRACTION	31	D	1 - 16
32	X-RAY DIFFRACTION	32	D	17 - 44
33	X-RAY DIFFRACTION	33	D	45 - 83
34	X-RAY DIFFRACTION	34	D	84 - 120
35	X-RAY DIFFRACTION	35	D	121 - 178
36	X-RAY DIFFRACTION	36	D	179 - 212
37	X-RAY DIFFRACTION	37	D	213 - 265
38	X-RAY DIFFRACTION	38	D	266 - 301
39	X-RAY DIFFRACTION	39	D	302 - 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