PDB-6uap: Crystal structure of tryptophan synthase from M. tuberculosis - o...

ID or keywords:

Entry

Database: PDB / ID: 6uap

Title

Crystal structure of tryptophan synthase from M. tuberculosis - open form with BRD6309 bound

Components

(Tryptophan synthase ...) x 2

Keywords

Lyase/Lyase Inhibitor / PLP / heterotetramer / amino acid biosynthesis / substrate channeling / allostery / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Lyase-Lyase Inhibitor complex

Function / homology

Function and homology information

tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / plasma membrane / cytosol / cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.745 Å

Authors

Chang, C. / Michalska, K. / Maltseva, N.I. / Jedrzejczak, R. / McCarren, P. / Nag, P.P. / Joachimiak, A. / Satchell, K. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

Canada, 1items

Citation

Journal: To be Published
Title: Crystal structure of tryptophan synthase from M. tuberculosis - open form with BRD6309 bound
Authors: Chang, C. / Michalska, K. / Maltseva, N.I. / Jedrzejczak, R. / McCarren, P. / Nag, P.P. / Joachimiak, A. / Satchell, K.

History

Deposition	Sep 11, 2019	Deposition site: RCSB / Processing site: RCSB
Supersession	Oct 30, 2019	ID: 6DU1
Revision 1.0	Oct 30, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 2, 2025	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6uap.cif.gz	963.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6uap.ent.gz	796.6 KB	Display	PDB format
PDBx/mmJSON format	6uap.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Similar structure data	5tcf-2 6e9p-2 5tch-2 4ht3-3 6u6c-1 5ocw-1 5tcg-1 5tci-1 1wbj-1 1tjp-1 5tcg-2 1k8x-1 6e9p-1 6xrh-1 5tcj-1 6xt0-1 6xoy-1 6usa-1 1qoq-1 2cll-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
Other databases	TargetTrack: CSGID-CPX_06552_06553

Similar structure data

Other databases

TargetTrack: CSGID-CPX_06552_06553

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (13) #154 - Oct 2012 Citric Acid Cycle similarity (1) #21 - Sep 2001 Antibodies similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1)

Deposited unit

A: Tryptophan synthase alpha chain

B: Tryptophan synthase beta chain

C: Tryptophan synthase alpha chain

D: Tryptophan synthase beta chain

E: Tryptophan synthase alpha chain

F: Tryptophan synthase beta chain

G: Tryptophan synthase alpha chain

H: Tryptophan synthase beta chain

hetero molecules

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

1

A: Tryptophan synthase alpha chain

B: Tryptophan synthase beta chain

G: Tryptophan synthase alpha chain

H: Tryptophan synthase beta chain

hetero molecules

defined by author&software
146 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Tryptophan synthase alpha chain

D: Tryptophan synthase beta chain

E: Tryptophan synthase alpha chain

F: Tryptophan synthase beta chain

hetero molecules

defined by author&software
146 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	134.777, 157.877, 166.690
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Tryptophan synthase ... , 2 types, 8 molecules ACEGBDFH

#1: Protein	Tryptophan synthase alpha chain Mass: 28579.449 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: trpA, Rv1613, MTCY01B2.05 / Plasmid: PMCSG81 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFY1, tryptophan synthase
#2: Protein	Tryptophan synthase beta chain Mass: 43562.711 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: trpB, Rv1612, MTCY01B2.04 / Plasmid: PMCSG81 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFX9, tryptophan synthase

#1: Protein

Tryptophan synthase alpha chain

Mass: 28579.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: trpA, Rv1613, MTCY01B2.05 / Plasmid: PMCSG81 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFY1, tryptophan synthase

#2: Protein

Tryptophan synthase beta chain

Mass: 43562.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: trpB, Rv1612, MTCY01B2.04 / Plasmid: PMCSG81 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFX9, tryptophan synthase

-
Non-polymers , 7 types, 345 molecules

#3: Chemical	... ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-H9V / (2R,3S,4R)-3-(4'-chloro-2',6'-difluoro[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile Mass: 336.739 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₁₂ClF₃N₂ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₄O₄
#7: Chemical	ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID Mass: 134.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₆O₅
#8: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₃O₂
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.08 Å³/Da / Density % sol: 60.1 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 8% TACSIMATE, 20% PEG3350, 5% PEG400, PH 8.0

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9788 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9788 Å / Relative weight: 1

Reflection

Resolution: 2.745→30 Å / Num. obs: 93179 / % possible obs: 99.7 % / Redundancy: 6 % / R_merge(I) obs: 0.165 / R_pim(I) all: 0.072 / R_rim(I) all: 0.181 / Χ²: 1.163 / Net I/σ(I): 5.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.745-2.8	5.7	1.12	4538	0.651	0.5	1.23	0.969	99.4
2.8-2.85	5.8	1.064	4590	0.685	0.472	1.167	0.983	99.3
2.85-2.9	5.8	0.912	4602	0.714	0.404	1	1.05	99.5
2.9-2.96	5.8	0.841	4609	0.753	0.372	0.922	1.027	99.7
2.96-3.03	5.8	0.703	4627	0.815	0.311	0.771	1.028	99.5
3.03-3.1	5.9	0.592	4580	0.85	0.261	0.648	1.038	99.6
3.1-3.17	5.9	0.497	4620	0.889	0.22	0.545	1.076	99.8
3.17-3.26	6	0.4	4624	0.916	0.176	0.438	1.056	100
3.26-3.36	6	0.325	4645	0.945	0.142	0.356	1.102	100
3.36-3.46	6.1	0.266	4648	0.964	0.116	0.291	1.105	100
3.46-3.59	6.1	0.223	4631	0.972	0.097	0.244	1.122	100
3.59-3.73	6.1	0.177	4651	0.985	0.076	0.193	1.182	100
3.73-3.9	6.2	0.149	4675	0.988	0.064	0.163	1.204	100
3.9-4.11	6.1	0.124	4664	0.992	0.054	0.136	1.266	100
4.11-4.36	6.1	0.107	4675	0.992	0.046	0.116	1.409	100
4.36-4.7	6.1	0.091	4680	0.994	0.039	0.099	1.562	100
4.7-5.17	6	0.089	4702	0.995	0.039	0.097	1.466	100
5.17-5.91	5.9	0.097	4741	0.994	0.043	0.106	1.231	99.8
5.91-7.43	5.9	0.066	4767	0.997	0.029	0.073	1.142	99.5
7.43-30	5.8	0.036	4910	0.999	0.016	0.039	1.177	98.9

-
Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.745→29.651 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.28

	R_factor	Num. reflection	% reflection
R_free	0.2114	1854	1.99 %
R_work	0.1708	-	-
obs	0.1716	93034	99.18 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 141.18 Å² / B_iso mean: 47.5968 Å² / B_iso min: 19.25 Å²

Refinement step

Cycle: final / Resolution: 2.745→29.651 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19150	0	259	302	19711
B_iso mean	-	-	64.07	38.39	-
Num. residues	-	-	-	-	2603

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.745-2.8141	0.3854	119	0.2806	6499	93
2.8141-2.8968	0.2948	153	0.2624	6918	99
2.8968-2.9903	0.3012	141	0.2492	6966	99
2.9903-3.097	0.3485	142	0.2382	6995	100
3.097-3.2209	0.2791	150	0.2272	6972	100
3.2209-3.3673	0.242	162	0.193	7011	100
3.3673-3.5445	0.208	139	0.171	7017	100
3.5445-3.7662	0.1958	154	0.157	7031	100
3.7662-4.0563	0.1855	148	0.145	7042	100
4.0563-4.4633	0.1937	151	0.1373	7068	100
4.4633-5.1063	0.1588	117	0.1308	7141	100
5.1063-6.4226	0.1767	154	0.1631	7152	100
6.4226-29.651	0.1549	124	0.1433	7368	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	0.596	0.0071	0.4683	0.6795	-0.1107	0.3962	0.0353	-0.0591	0.0744	0.0202	0.0265	-0.2435	0.0966	-0.0466	-0	0.3188	-0.0079	0.0249	0.2992	-0.0017	0.4266	88.7584	-12.9581	22.1913
2	0.2824	0.1488	0.0776	0.2299	-0.205	0.4329	-0.0893	0.2551	0.2419	-0.023	0.0858	-0.1442	-0.2113	0.0327	0	0.2148	-0.0184	0.0062	0.2708	0.0074	0.3949	84.4185	-2.181	20.066
3	0.2216	-0.0607	0.1815	0.1503	0.0312	0.0647	0.0566	0.6581	-0.0789	-0.153	-0.0687	-0.4605	-0.0696	0.0226	0.0004	0.3012	-0.0196	0.0368	0.421	0.0109	0.4308	78.545	-8.4231	8.1609
4	0.5897	-0.3153	-0.3002	0.5918	0.349	0.2219	0.0492	0.2422	-0.2958	0.0454	-0.1223	-0.1703	0.3485	-0.0316	-0.0061	0.3199	0.0215	0.0175	0.3602	-0.0678	0.4566	88.7076	-23.6102	15.183
5	0.0316	-0.0855	0.0036	0.1696	-0.0132	0.0052	-0.1118	0.4051	-0.0984	-0.2164	0.3237	0.0552	-0.2296	0.0871	0.0009	0.3926	0.0224	0.0102	0.4893	0.0437	0.3937	57.6775	0.362	13.4554
6	0.0866	-0.0038	0.1462	0.2031	0.0769	0.2251	0.0027	0.3656	-0.1246	-0.0224	-0.0019	0.016	0.077	0.0914	-0	0.3483	-0.0028	0.0421	0.367	0.0657	0.264	48.0606	-13.1512	12.4807
7	0.0837	-0.2251	-0.2991	0.5578	-0.2143	0.4981	0.0032	-0.1487	-0.1125	0.0548	-0.0945	0.027	-0.0316	0.173	-0	0.2526	-0.0244	-0.0153	0.3396	0.0175	0.2862	49.9975	-14.1703	30.9287
8	0.1743	0.0642	-0.4449	0.4329	-0.1163	1.0443	0.0509	0.0651	-0.0428	-0.0927	-0.0117	-0.038	-0.1111	0.039	0	0.213	0.0089	-0.0118	0.2408	0.0097	0.1953	49.9439	0.5431	26.6895
9	0.2277	0.1288	-0.1377	0.0432	-0.0836	0.0162	0.1078	-0.2029	0.0828	0.1215	0.0528	-0.1758	-0.1089	0.0124	0	0.2919	-0.011	-0.0141	0.3249	-0.0076	0.3183	62.441	1.0366	29.7745
10	0.1243	-0.1306	-0.0476	0.069	0.0824	0.0483	0.0094	-0.2215	0.154	0.1667	-0.0573	-0.2047	-0.1155	-0.015	-0	0.3113	-0.0511	-0.0193	0.3257	0.0416	0.2961	47.0551	3.2646	44.2144
11	0.3546	0.315	-0.0955	0.1567	-0.0143	0.2361	-0.0861	0.0997	-0.0129	0.0533	0.1056	-0.0693	0.0274	0.0365	0	0.3006	-0.0114	0.0132	0.1987	0.0171	0.2217	44.9179	-0.282	43.569
12	0.5363	0.1045	0.238	0.7367	0.0134	0.0808	0.0973	0.0391	0.0402	-0.0971	-0.0032	0.3783	0.139	-0.0394	-0	0.2954	0.0293	0.0054	0.3597	-0.0363	0.451	-21.1322	14.04	9.8171
13	0.0569	0.1447	0.0956	0.2583	0.0675	0.242	0.2051	0.1496	0.1066	0.0061	-0.0041	0.1706	-0.064	0.0452	0	0.2571	0.0361	0.0386	0.3214	-0.0159	0.3774	-13.5642	23.5958	10.3495
14	0.3073	-0.0418	-0.241	0.2277	0.1903	0.2526	0.0788	-0.2184	-0.1253	0.1063	0.0327	0.0818	-0.0192	0.0706	0	0.3237	0.0054	0.062	0.395	-0.0241	0.4124	-9.7443	13.7496	22.5807
15	0.8211	-0.2467	-0.5024	0.4735	-0.145	0.319	-0.0504	-0.1673	-0.2693	0.0493	0.0073	0.4021	0.1526	-0.231	0	0.2628	-0.0424	0.0081	0.4137	0.0144	0.5702	-25.7955	4.8645	17.6054
16	0.0966	-0.0281	-0.1428	-0.0347	0.0186	0.0749	-0.0212	-0.3497	0.0336	0.0685	0.0688	-0.1047	-0.3561	0.0478	0.0004	0.3332	-0.0834	0.0508	0.3959	-0.0828	0.372	13.4484	10.9912	18.9914
17	0.0409	-0.0164	0.0622	0.2	0.0101	0.0889	0.0242	-0.3136	0.1367	0.0837	0.1311	-0.1122	0.0847	0.0524	0	0.3096	-0.022	0.0012	0.3627	-0.0229	0.3047	14.8405	-4.7971	20.0747
18	0.41	0.0085	-0.2218	0.5	0.6448	0.7971	0.0851	0.0689	-0.1263	-0.09	-0.1761	0.0327	-0.106	-0.1565	-0.0045	0.2314	0.0218	-0.0119	0.2878	-0.0301	0.2286	11.8159	-4.704	2.9025
19	0.2627	0.0979	-0.4377	0.4829	0.2669	0.8809	0.0602	-0.0054	-0.0059	-0.0996	-0.0015	-0.022	-0.1344	-0.0102	-0	0.2384	-0.0187	0.0219	0.2225	-0.0064	0.2423	19.6535	9.3289	-1.8362
20	0.311	0.3714	-0.1429	1.2889	-0.188	0.6879	-0.0094	0.6627	0.2098	-1.5686	0.4731	0.2276	0.1738	0.061	0.8712	0.9641	-0.1826	0.5103	0.6446	-0.3636	0.2262	41.3174	-39.8369	-53.7052
21	0.4373	0.2867	-0.0745	0.7312	0.0672	0.3571	-0.1868	0.1138	0.0133	-0.3103	0.1639	-0.2139	-0.0132	0.046	-0	0.5512	-0.0286	0.1144	0.4021	-0.1023	0.3793	37.4451	-40.6932	-41.0097
22	0.0906	0.1006	0.1223	0.0649	0.1058	0.0826	0.3826	0.0687	-0.258	-0.3722	-0.161	-0.0534	-0.1905	0.389	0.0007	0.6176	-0.0255	0.2104	0.5172	-0.1868	0.7923	50.7298	-39.3493	-36.6989
23	0.1953	0.0587	-0.2991	0.9383	0.0248	0.3189	-0.139	0.3014	0.0471	-0.7115	0.3309	-0.3204	-0.0249	0.3683	0.0486	0.7805	-0.1571	0.2674	0.6218	-0.0548	0.446	46.6645	-28.7479	-51.1664
24	0.1226	-0.0706	-0.0879	0.0036	0.0261	0.0389	-0.115	0.2547	-0.4884	-0.1732	0.0568	-0.1981	0.086	0.3674	-0	0.3838	0.0901	0.0248	0.5122	-0.019	0.4774	47.2734	-33.8694	-17.2964
25	0.369	-0.0627	-0.0038	0.1556	-0.0811	0.0683	0.0092	-0.1931	0.1498	-0.0464	0.222	-0.3599	-0.0406	0.3728	-0	0.2285	0.001	0.0442	0.4155	-0.0297	0.3749	48.3731	-15.56	-14.8064
26	0.3439	-0.3534	0.2891	0.2173	-0.2348	0.1924	0.0076	0.0178	0.0633	0.0143	0.0579	-0.0171	-0.0197	-0.0908	0	0.2885	-0.0282	0.0318	0.2532	-0.0295	0.2752	31.2731	-16.7435	-7.9021
27	0.2908	-0.4744	-0.3817	0.5089	0.0603	0.5841	0.0788	0.1393	-0.0932	-0.1478	-0.0721	0.1343	0.0451	-0.0517	-0	0.295	-0.0004	0.0344	0.2601	-0.0147	0.2849	30.7239	-16.8723	-26.3819
28	0.5652	-0.0147	-0.3606	0.3456	0.0288	0.2597	-0.0581	-0.0194	-0.037	-0.0768	-0.042	-0.0755	0.0527	-0.068	0	0.3093	-0.0017	0.0007	0.2093	-0.0258	0.2725	32.8216	-32.4135	-10.3079
29	-0.0235	-0.0347	-0.0017	0.2064	-0.0945	0.0179	0.0682	0.1738	-0.0114	-0.0312	-0.0811	0.1579	0.1696	-0.2574	-0	0.2746	-0.0554	0.0176	0.2775	-0.035	0.3398	17.4318	-30.2815	-3.5936
30	0.1823	0.0014	-0.2316	0.4642	0.3403	0.271	0.0896	-0.0048	-0.1039	-0.0566	-0.0137	-0.0144	0.0833	-0.061	0	0.2663	-0.0027	-0.0003	0.2194	-0.0214	0.265	18.6103	-26.3703	-3.214
31	0.4774	-0.024	0.6197	0.7918	-0.1382	0.5548	-0.1067	-0.0755	-0.0767	0.4604	0.0389	0.0334	-0.2865	-0.0302	-0.0008	0.496	-0.0177	0.0772	0.275	0.0413	0.2921	12.1378	-31.9053	81.3273
32	0.7382	-0.2615	-0.1128	0.8214	-0.4617	0.3979	0.0183	-0.0496	-0.0707	0.5336	0.1171	0.2748	-0.2057	-0.2183	0.022	0.4734	-0.0159	0.1067	0.2504	0.0143	0.2821	6.8697	-23.3824	77.7489
33	0.0286	0.0073	0.0474	0.0542	-0.0329	0.0961	-0.0126	0.0958	-0.0581	0.1763	-0.3199	0.2503	-0.1515	-0.6065	-0	0.2818	-0.0097	-0.0052	0.4592	0.0157	0.342	5.7785	-23.0913	50.456
34	0.2321	-0.2046	0.1023	0.3157	0.044	0.1793	0.2445	0.2726	0.1809	0.1184	0.1653	0.2795	-0.3482	-0.3613	0	0.3679	0.03	0.0034	0.409	0.0232	0.351	13.5073	-6.2265	47.3
35	0.2146	0.3798	0.0191	0.4666	0.1536	0.6403	0.0762	-0.0064	-0.0188	0.0268	-0.0481	-0.034	-0.0041	-0.0418	-0	0.2483	-0.0133	-0.0143	0.2602	0.0191	0.2525	25.9393	-16.8704	45.7122
36	0.1608	0.1434	-0.1596	0.0164	-0.0625	0.0635	-0.1293	0.1749	-0.2406	0.0025	-0.1113	0.0354	0.1158	-0.0923	0	0.3481	-0.033	0.0231	0.3515	0.0245	0.3557	20.8249	-35.2241	44.4091
37	0.162	-0.163	-0.1115	0.0811	-0.0061	0.2806	-0.1103	-0.0222	-0.0325	0.1094	-0.0072	0.1799	0.1021	0.0414	0	0.3576	-0.0424	0.0409	0.3268	0.0201	0.3582	18.8695	-32.0207	51.874
38	0.4194	0.0706	-0.2987	0.598	-0.2488	0.1632	0.0716	-0.0955	-0.1152	0.0796	-0.0009	-0.1049	0.0932	0.0853	0	0.2731	-0.0117	-0.0109	0.2618	0.0365	0.2789	34.2324	-31.3711	36.3184

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 85 )	A	8 - 85
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 86 through 142 )	A	86 - 142
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 143 through 197 )	A	143 - 197
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 198 through 267 )	A	198 - 267
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 5 through 31 )	B	5 - 31
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 32 through 64 )	B	32 - 64
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 65 through 194 )	B	65 - 194
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 195 through 293 )	B	195 - 293
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 294 through 336 )	B	294 - 336
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 337 through 357 )	B	337 - 357
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 358 through 409 )	B	358 - 409
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 9 through 85 )	C	9 - 85
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 86 through 126 )	C	86 - 126
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 127 through 197 )	C	127 - 197
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 198 through 267 )	C	198 - 267
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 4 through 31 )	D	4 - 31
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 32 through 64 )	D	32 - 64
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 65 through 210 )	D	65 - 210
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 211 through 409 )	D	211 - 409
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 9 through 50 )	E	9 - 50
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 51 through 142 )	E	51 - 142
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 143 through 165 )	E	143 - 165
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 166 through 266 )	E	166 - 266
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 8 through 31 )	F	8 - 31
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 32 through 64 )	F	32 - 64
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 65 through 140 )	F	65 - 140
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 141 through 210 )	F	141 - 210
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 211 through 336 )	F	211 - 336
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 337 through 357 )	F	337 - 357
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 358 through 407 )	F	358 - 407
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 9 through 108 )	G	9 - 108
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 109 through 266 )	G	109 - 266
33	X-RAY DIFFRACTION	33	chain 'H' and (resid 9 through 31 )	H	9 - 31
34	X-RAY DIFFRACTION	34	chain 'H' and (resid 32 through 64 )	H	32 - 64
35	X-RAY DIFFRACTION	35	chain 'H' and (resid 65 through 258 )	H	65 - 258
36	X-RAY DIFFRACTION	36	chain 'H' and (resid 259 through 293 )	H	259 - 293
37	X-RAY DIFFRACTION	37	chain 'H' and (resid 294 through 335 )	H	294 - 335
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 336 through 408 )	H	336 - 408

-
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

-
Tryptophan synthase ... , 2 types, 8 molecules ACEGBDFH

-
Non-polymers , 7 types, 345 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Tryptophan synthase ... , 2 types, 8 molecules ACEGBDFH

-Non-polymers , 7 types, 345 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Tryptophan synthase ... , 2 types, 8 molecules ACEGBDFH

-
Non-polymers , 7 types, 345 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi