PDB-4fox: Crystal Structure of Mtb ThyA in complex with dUMP and Raltitrexed

ID or keywords:

Entry

Database: PDB / ID: 4fox

Title

Crystal Structure of Mtb ThyA in complex with dUMP and Raltitrexed

Components

Thymidylate synthase

Keywords

TRANSFERASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / thymidylate synthase

Function / homology

Function and homology information

dUMP catabolic process / thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / response to antibiotic / cytoplasm / cytosol
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.3 Å

Authors

Reddy, M.C.M. / Bruning, J.B. / Sacchettini, J.C. / Harshbarger, W. / TB Structural Genomics Consortium (TBSGC)

Citation

Journal: To be Published
Title: Crystal structure of binary and ternary complexes of thymidylate synthase (ThyA) from Mycobacterium tuberculosis: Insights into the selectivity and mode of inhibition
Authors: Reddy, M.C.M. / Bruning, J.B. / Sacchettini, J.C. / Harshbarger, W.

History

Deposition	Jun 21, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	4fox.cif.gz	850.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4fox.ent.gz	711.4 KB	Display	PDB format
PDBx/mmJSON format	4fox.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4fox_validation.pdf.gz	4.4 MB	Display	wwPDB validaton report
Full document	4fox_full_validation.pdf.gz	4.4 MB	Display
Data in XML	4fox_validation.xml.gz	85.5 KB	Display
Data in CIF	4fox_validation.cif.gz	108.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fo/4fox ftp://data.pdbj.org/pub/pdb/validation_reports/fo/4fox	HTTPS FTP

-
Related structure data

Related structure data	4foaC 4fogC 3qj7S 4fqs S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2a9w-2 1f4b-1 1tdu-d 2ftq-1 1f4e-1 4fog-2 4isk-4 1ev5-1 1f4d-d 2vet-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) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Thymidylate synthase

B: Thymidylate synthase

C: Thymidylate synthase

D: Thymidylate synthase

E: Thymidylate synthase

F: Thymidylate synthase

G: Thymidylate synthase

H: Thymidylate synthase

hetero molecules

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

1

A: Thymidylate synthase

B: Thymidylate synthase

hetero molecules

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

2

C: Thymidylate synthase

D: Thymidylate synthase

hetero molecules

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

3

E: Thymidylate synthase

F: Thymidylate synthase

hetero molecules

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

4

G: Thymidylate synthase

H: Thymidylate synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	91.342, 138.444, 99.948
Angle α, β, γ (deg.)	90.000, 107.000, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Thymidylate synthase / TS / TSase Mass: 29884.830 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT2834, MTV002.29c, Rv2764c, thyA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P67044, UniProt: P9WFR9*PLUS, thymidylate synthase
#2: Chemical	ChemComp-D16 / TOMUDEX / ZD1694 / Raltitrexed Mass: 458.488 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₂N₄O₆S / Comment: chemotherapy, inhibitor*YM
#3: Chemical	ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP Mass: 308.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₉H₁₃N₂O₈P
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.53 Å³/Da / Density % sol: 51.34 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 2M ammonium sulfate, 0.1M imidazole 6.4, 5mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 0.91924 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 10, 2010 / Details: mirrors

Radiation

Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.91924 Å / Relative weight: 1

Reflection

Redundancy: 4.05 % / Number: 420756 / R_merge(I) obs: 0.112 / Χ²: 1 / D res high: 2.3 Å / D res low: 69.22 Å / Num. obs: 102988 / % possible obs: 97.8

Diffraction reflection shell

ID: 1

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	R_merge(I) obs	Chi squared	Redundancy	Rejects
4.95	69.22	98.6	0.084	1.47	4.29	2202
3.93	4.95	99.7	0.094	1.13	4.27	209
3.44	3.93	98.8	0.129	1.46	3.88	562
3.12	3.44	98.2	0.13	1.06	3.95	62
2.9	3.12	97.6	0.156	0.95	3.99	10
2.73	2.9	97.4	0.186	0.86	4.01	6
2.59	2.73	97.1	0.268	0.97	3.92	97
2.48	2.59	97.2	0.271	0.72	4.07
2.38	2.48	96.6	0.319	0.66	4.08	3
2.3	2.38	96.5	0.363	0.64	4.09	5

Reflection

Resolution: 2.3→69.22 Å / Num. all: 102988 / Num. obs: 102988 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.05 % / B_iso Wilson estimate: 48.43 Å² / R_merge(I) obs: 0.112 / R_sym value: 0.112 / Χ²: 1 / Net I/σ(I): 7.6 / Scaling rejects: 3156

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	Χ²	% possible all
2.3-2.38	4.09	0.363	2.8	41457	10135	0.64	96.5
2.38-2.48	4.08	0.319	3.2	41427	10152	0.66	96.6
2.48-2.59	4.07	0.271	3.7	41434	10187	0.72	97.2
2.59-2.73	3.92	0.268	4.1	39971	10178	0.97	97.1
2.73-2.9	4.01	0.186	5.4	41111	10239	0.86	97.4
2.9-3.12	3.99	0.156	6.6	41043	10278	0.95	97.6
3.12-3.44	3.95	0.13	8.3	40817	10329	1.06	98.2
3.44-3.93	3.88	0.129	9.9	40969	10423	1.46	98.8
3.93-4.95	4.27	0.094	13.2	45201	10542	1.13	99.7
4.95-69.22	4.29	0.084	17.1	47326	10525	1.47	98.6

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
d*TREK		data scaling
d*TREK	9.7 W8RSSI	data reduction
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3QJ7

3qj7

Resolution: 2.3→45.0089 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7946 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: mlhl

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2577	5139	4.99 %	random
R_work	0.2126	-	-	-
all	0.2149	102895	-	-
obs	0.2149	102895	97.7 %	-

Solvent computation

B_sol: 49.64 Å² / k_sol: 0.347 e/Å³

Displacement parameters

B_iso max: 178.13 Å² / B_iso mean: 57.2676 Å² / B_iso min: 20 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.237 Å²	0 Å²	2.115 Å²
2-	-	-0.832 Å²	-0 Å²
3-	-	-	-4.405 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→45.0089 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16473	0	416	352	17241

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	0.767	1
X-RAY DIFFRACTION	f_bond_d	0.006	1
X-RAY DIFFRACTION	f_chiral_restr	0.056	1
X-RAY DIFFRACTION	f_dihedral_angle_d	11.29	1
X-RAY DIFFRACTION	f_plane_restr	0.004	1
X-RAY DIFFRACTION	f_nbd_refined	4.08	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
2.3-2.3039	0.2782	503	X-RAY DIFFRACTION	196	91
2.3039-2.3079	0.2724	459	X-RAY DIFFRACTION	196	90
2.3079-2.3119	0.2863	477	X-RAY DIFFRACTION	196	91
2.3119-2.3159	0.2681	512	X-RAY DIFFRACTION	196	91
2.3159-2.3199	0.2509	471	X-RAY DIFFRACTION	196	92
2.3199-2.324	0.2453	522	X-RAY DIFFRACTION	196	92
2.324-2.3281	0.2469	478	X-RAY DIFFRACTION	196	91
2.3281-2.3322	0.2626	501	X-RAY DIFFRACTION	196	92
2.3322-2.3363	0.2561	518	X-RAY DIFFRACTION	196	94
2.3363-2.3405	0.2539	491	X-RAY DIFFRACTION	196	92
2.3405-2.3447	0.2546	476	X-RAY DIFFRACTION	196	90
2.3447-2.349	0.2433	482	X-RAY DIFFRACTION	196	93
2.349-2.3532	0.2565	463	X-RAY DIFFRACTION	196	94
2.3532-2.3575	0.2567	526	X-RAY DIFFRACTION	196	91
2.3575-2.3619	0.2491	501	X-RAY DIFFRACTION	196	94
2.3619-2.3662	0.2362	484	X-RAY DIFFRACTION	196	91
2.3662-2.3706	0.2642	499	X-RAY DIFFRACTION	196	92
2.3706-2.375	0.2559	524	X-RAY DIFFRACTION	196	94
2.375-2.3795	0.2411	476	X-RAY DIFFRACTION	196	91
2.3795-2.384	0.2515	479	X-RAY DIFFRACTION	196	92
2.384-2.3885	0.2452	482	X-RAY DIFFRACTION	196	90
2.3885-2.3931	0.2471	511	X-RAY DIFFRACTION	196	92
2.3931-2.3977	0.2505	466	X-RAY DIFFRACTION	196	90
2.3977-2.4023	0.2547	504	X-RAY DIFFRACTION	196	92
2.4023-2.407	0.2551	495	X-RAY DIFFRACTION	196	92
2.407-2.4117	0.2648	502	X-RAY DIFFRACTION	196	92
2.4117-2.4165	0.27	451	X-RAY DIFFRACTION	196	92
2.4165-2.4213	0.2652	471	X-RAY DIFFRACTION	196	89
2.4213-2.4261	0.249	535	X-RAY DIFFRACTION	196	92
2.4261-2.4309	0.2662	486	X-RAY DIFFRACTION	196	91
2.4309-2.4358	0.2494	516	X-RAY DIFFRACTION	196	92
2.4358-2.4408	0.2551	472	X-RAY DIFFRACTION	196	93
2.4408-2.4458	0.2585	466	X-RAY DIFFRACTION	196	90
2.4458-2.4508	0.2592	498	X-RAY DIFFRACTION	196	93
2.4508-2.4559	0.2506	479	X-RAY DIFFRACTION	196	90
2.4559-2.461	0.2612	496	X-RAY DIFFRACTION	196	93
2.461-2.4661	0.2629	489	X-RAY DIFFRACTION	196	92
2.4661-2.4713	0.2392	529	X-RAY DIFFRACTION	196	92
2.4713-2.4765	0.2393	507	X-RAY DIFFRACTION	196	92
2.4765-2.4818	0.241	468	X-RAY DIFFRACTION	196	92
2.4818-2.4871	0.2595	477	X-RAY DIFFRACTION	196	94
2.4871-2.4925	0.256	504	X-RAY DIFFRACTION	196	92
2.4925-2.4979	0.2322	480	X-RAY DIFFRACTION	196	91
2.4979-2.5034	0.2584	497	X-RAY DIFFRACTION	196	92
2.5034-2.5089	0.2304	489	X-RAY DIFFRACTION	196	93
2.5089-2.5145	0.2409	530	X-RAY DIFFRACTION	196	94
2.5145-2.5201	0.2584	488	X-RAY DIFFRACTION	196	92
2.5201-2.5257	0.2422	490	X-RAY DIFFRACTION	196	92
2.5257-2.5314	0.2402	505	X-RAY DIFFRACTION	196	94
2.5314-2.5372	0.2249	495	X-RAY DIFFRACTION	196	92
2.5372-2.543	0.2479	485	X-RAY DIFFRACTION	196	93
2.543-2.5489	0.2401	504	X-RAY DIFFRACTION	196	92
2.5489-2.5548	0.2277	512	X-RAY DIFFRACTION	196	94
2.5548-2.5608	0.238	520	X-RAY DIFFRACTION	196	93
2.5608-2.5669	0.2484	431	X-RAY DIFFRACTION	196	91
2.5669-2.5729	0.2396	482	X-RAY DIFFRACTION	196	92
2.5729-2.5791	0.2358	528	X-RAY DIFFRACTION	196	92
2.5791-2.5853	0.2453	498	X-RAY DIFFRACTION	196	92
2.5853-2.5916	0.2542	494	X-RAY DIFFRACTION	196	92
2.5916-2.5979	0.2611	478	X-RAY DIFFRACTION	196	94
2.5979-2.6043	0.2367	500	X-RAY DIFFRACTION	196	89
2.6043-2.6108	0.2444	503	X-RAY DIFFRACTION	196	93
2.6108-2.6173	0.2476	498	X-RAY DIFFRACTION	196	92
2.6173-2.6239	0.2487	484	X-RAY DIFFRACTION	196	93
2.6239-2.6306	0.2612	497	X-RAY DIFFRACTION	196	93
2.6306-2.6373	0.2643	480	X-RAY DIFFRACTION	196	94
2.6373-2.6441	0.2665	502	X-RAY DIFFRACTION	196	93
2.6441-2.6509	0.2561	515	X-RAY DIFFRACTION	196	92
2.6509-2.6579	0.2672	473	X-RAY DIFFRACTION	196	91
2.6579-2.6649	0.2632	513	X-RAY DIFFRACTION	196	94
2.6649-2.672	0.2734	503	X-RAY DIFFRACTION	196	93
2.672-2.6791	0.2721	487	X-RAY DIFFRACTION	196	91
2.6791-2.6864	0.2963	486	X-RAY DIFFRACTION	196	91
2.6864-2.6937	0.2704	486	X-RAY DIFFRACTION	196	91
2.6937-2.7011	0.2594	530	X-RAY DIFFRACTION	196	95
2.7011-2.7086	0.248	497	X-RAY DIFFRACTION	196	93
2.7086-2.7161	0.2555	474	X-RAY DIFFRACTION	196	92
2.7161-2.7238	0.2464	469	X-RAY DIFFRACTION	196	89
2.7238-2.7315	0.2524	497	X-RAY DIFFRACTION	196	92
2.7315-2.7394	0.254	456	X-RAY DIFFRACTION	196	91
2.7394-2.7473	0.2672	523	X-RAY DIFFRACTION	196	93
2.7473-2.7553	0.2456	518	X-RAY DIFFRACTION	196	93
2.7553-2.7634	0.2453	505	X-RAY DIFFRACTION	196	92
2.7634-2.7716	0.2588	511	X-RAY DIFFRACTION	196	91
2.7716-2.7799	0.2694	476	X-RAY DIFFRACTION	196	94
2.7799-2.7883	0.2365	469	X-RAY DIFFRACTION	196	93
2.7883-2.7968	0.2542	532	X-RAY DIFFRACTION	196	94
2.7968-2.8054	0.2431	479	X-RAY DIFFRACTION	196	93
2.8054-2.8141	0.2521	459	X-RAY DIFFRACTION	196	91
2.8141-2.8229	0.2411	508	X-RAY DIFFRACTION	196	93
2.8229-2.8318	0.2465	522	X-RAY DIFFRACTION	196	94
2.8318-2.8409	0.2306	509	X-RAY DIFFRACTION	196	92
2.8409-2.85	0.2546	524	X-RAY DIFFRACTION	196	93
2.85-2.8593	0.252	470	X-RAY DIFFRACTION	196	94
2.8593-2.8687	0.2333	500	X-RAY DIFFRACTION	196	93
2.8687-2.8783	0.253	478	X-RAY DIFFRACTION	196	94
2.8783-2.8879	0.2331	499	X-RAY DIFFRACTION	196	92
2.8879-2.8977	0.2298	492	X-RAY DIFFRACTION	196	92
2.8977-2.9076	0.2422	510	X-RAY DIFFRACTION	196	92
2.9076-2.9177	0.236	500	X-RAY DIFFRACTION	196	94
2.9177-2.9279	0.2551	479	X-RAY DIFFRACTION	196	90
2.9279-2.9382	0.2301	524	X-RAY DIFFRACTION	196	94
2.9382-2.9487	0.2452	483	X-RAY DIFFRACTION	196	92
2.9487-2.9594	0.2425	508	X-RAY DIFFRACTION	196	93
2.9594-2.9702	0.2292	487	X-RAY DIFFRACTION	196	95
2.9702-2.9811	0.2392	464	X-RAY DIFFRACTION	196	92
2.9811-2.9922	0.2342	514	X-RAY DIFFRACTION	196	92
2.9922-3.0035	0.221	513	X-RAY DIFFRACTION	196	93
3.0035-3.015	0.2235	494	X-RAY DIFFRACTION	196	92
3.015-3.0266	0.2335	476	X-RAY DIFFRACTION	196	93
3.0266-3.0384	0.2254	535	X-RAY DIFFRACTION	196	95
3.0384-3.0504	0.2449	474	X-RAY DIFFRACTION	196	93
3.0504-3.0626	0.2662	507	X-RAY DIFFRACTION	196	95
3.0626-3.075	0.2463	523	X-RAY DIFFRACTION	196	92
3.075-3.0876	0.2482	479	X-RAY DIFFRACTION	196	94
3.0876-3.1004	0.2454	514	X-RAY DIFFRACTION	196	95
3.1004-3.1135	0.2429	476	X-RAY DIFFRACTION	196	92
3.1135-3.1267	0.2524	519	X-RAY DIFFRACTION	196	92
3.1267-3.1402	0.2481	516	X-RAY DIFFRACTION	196	95
3.1402-3.1539	0.2313	495	X-RAY DIFFRACTION	196	93
3.1539-3.1678	0.217	499	X-RAY DIFFRACTION	196	94
3.1678-3.182	0.2168	481	X-RAY DIFFRACTION	196	91
3.182-3.1965	0.2285	490	X-RAY DIFFRACTION	196	93
3.1965-3.2112	0.2072	508	X-RAY DIFFRACTION	196	93
3.2112-3.2262	0.2291	500	X-RAY DIFFRACTION	196	93
3.2262-3.2415	0.2174	514	X-RAY DIFFRACTION	196	93
3.2415-3.2571	0.2283	512	X-RAY DIFFRACTION	196	93
3.2571-3.273	0.2092	493	X-RAY DIFFRACTION	196	94
3.273-3.2892	0.21	493	X-RAY DIFFRACTION	196	94
3.2892-3.3057	0.2047	499	X-RAY DIFFRACTION	196	95
3.3057-3.3225	0.189	510	X-RAY DIFFRACTION	196	93
3.3225-3.3398	0.2105	524	X-RAY DIFFRACTION	196	94
3.3398-3.3573	0.2153	488	X-RAY DIFFRACTION	196	94
3.3573-3.3753	0.2054	520	X-RAY DIFFRACTION	196	94
3.3753-3.3936	0.2004	483	X-RAY DIFFRACTION	196	94
3.3936-3.4124	0.2035	515	X-RAY DIFFRACTION	196	93
3.4124-3.4315	0.1981	485	X-RAY DIFFRACTION	196	93
3.4315-3.4511	0.2028	535	X-RAY DIFFRACTION	196	94
3.4511-3.4712	0.2213	486	X-RAY DIFFRACTION	196	93
3.4712-3.4917	0.2003	484	X-RAY DIFFRACTION	196	94
3.4917-3.5127	0.2143	532	X-RAY DIFFRACTION	196	93
3.5127-3.5343	0.2028	483	X-RAY DIFFRACTION	196	93
3.5343-3.5563	0.185	530	X-RAY DIFFRACTION	196	94
3.5563-3.579	0.2038	483	X-RAY DIFFRACTION	196	93
3.579-3.6022	0.1929	486	X-RAY DIFFRACTION	196	93
3.6022-3.6261	0.1932	505	X-RAY DIFFRACTION	196	95
3.6261-3.6505	0.1978	529	X-RAY DIFFRACTION	196	94
3.6505-3.6757	0.1831	499	X-RAY DIFFRACTION	196	92
3.6757-3.7016	0.1947	476	X-RAY DIFFRACTION	196	92
3.7016-3.7282	0.1946	516	X-RAY DIFFRACTION	196	96
3.7282-3.7556	0.1926	518	X-RAY DIFFRACTION	196	94
3.7556-3.7838	0.1873	500	X-RAY DIFFRACTION	196	95
3.7838-3.8129	0.188	519	X-RAY DIFFRACTION	196	94
3.8129-3.8429	0.196	522	X-RAY DIFFRACTION	196	95
3.8429-3.8739	0.1986	480	X-RAY DIFFRACTION	196	91
3.8739-3.9059	0.1907	474	X-RAY DIFFRACTION	196	94
3.9059-3.939	0.1992	541	X-RAY DIFFRACTION	196	94
3.939-3.9732	0.188	509	X-RAY DIFFRACTION	196	94
3.9732-4.0086	0.1838	485	X-RAY DIFFRACTION	196	95
4.0086-4.0454	0.1802	536	X-RAY DIFFRACTION	196	95
4.0454-4.0835	0.1682	488	X-RAY DIFFRACTION	196	94
4.0835-4.1232	0.1557	511	X-RAY DIFFRACTION	196	96
4.1232-4.1644	0.1645	535	X-RAY DIFFRACTION	196	93
4.1644-4.2073	0.1519	488	X-RAY DIFFRACTION	196	95
4.2073-4.252	0.1478	496	X-RAY DIFFRACTION	196	93
4.252-4.2987	0.1354	511	X-RAY DIFFRACTION	196	94
4.2987-4.3475	0.1422	530	X-RAY DIFFRACTION	196	94
4.3475-4.3986	0.1253	498	X-RAY DIFFRACTION	196	94
4.3986-4.4522	0.125	488	X-RAY DIFFRACTION	196	95
4.4522-4.5085	0.1414	534	X-RAY DIFFRACTION	196	95
4.5085-4.5678	0.136	505	X-RAY DIFFRACTION	196	95
4.5678-4.6303	0.1458	504	X-RAY DIFFRACTION	196	93
4.6303-4.6963	0.1502	490	X-RAY DIFFRACTION	196	94
4.6963-4.7664	0.1279	537	X-RAY DIFFRACTION	196	94
4.7664-4.8408	0.1488	478	X-RAY DIFFRACTION	196	93
4.8408-4.92	0.14	509	X-RAY DIFFRACTION	196	94
4.92-5.0048	0.1508	523	X-RAY DIFFRACTION	196	95
5.0048-5.0957	0.154	509	X-RAY DIFFRACTION	196	95
5.0957-5.1935	0.1439	526	X-RAY DIFFRACTION	196	95
5.1935-5.2994	0.1614	516	X-RAY DIFFRACTION	196	95
5.2994-5.4144	0.1471	512	X-RAY DIFFRACTION	196	94
5.4144-5.5401	0.1639	509	X-RAY DIFFRACTION	196	95
5.5401-5.6784	0.1652	519	X-RAY DIFFRACTION	196	96
5.6784-5.8317	0.1707	501	X-RAY DIFFRACTION	196	95
5.8317-6.0029	0.1644	519	X-RAY DIFFRACTION	196	95
6.0029-6.1962	0.1805	514	X-RAY DIFFRACTION	196	96
6.1962-6.417	0.189	509	X-RAY DIFFRACTION	196	93
6.417-6.6732	0.1752	533	X-RAY DIFFRACTION	196	95
6.6732-6.9758	0.1791	501	X-RAY DIFFRACTION	196	95
6.9758-7.3421	0.1628	515	X-RAY DIFFRACTION	196	94
7.3421-7.7999	0.1611	519	X-RAY DIFFRACTION	196	95
7.7999-8.3985	0.1738	507	X-RAY DIFFRACTION	196	94
8.3985-9.2371	0.1759	511	X-RAY DIFFRACTION	196	93
9.2371-10.5587	0.1763	490	X-RAY DIFFRACTION	196	89
10.5587-13.2464	0.1779	491	X-RAY DIFFRACTION	196	89
13.2464-45.0175	0.3011	422	X-RAY DIFFRACTION	196	75

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	0.5174	0.6258	0.112	1.31	0.5094	1.2506	0.1164	-0.1082	0.0944	0.2603	-0.1406	0.2576	0.0224	-0.1999	0.0205	0.3308	-0.0772	0.0038	0.2357	-0.0077	0.3007	-22.8484	-14.3386	48.5831
2	0.8752	-0.3626	0.7937	1.2174	0.8479	0.1814	0.166	0.1227	0.1787	-0.5195	-0.0949	0.1439	-0.4374	0.0995	-0.0203	0.4074	-0.0097	0.0087	0.2095	0.047	0.2567	-18.5491	-3.6192	35.3796
3	0.3662	-0.1672	-0.0218	2.0374	1.2594	0.8252	0.0742	0.0302	-0.085	0.2112	-0.2081	0.1992	-0.1355	-0.1621	0.1281	0.319	-0.0811	-0.0244	0.2262	0.021	0.2251	-18.2785	-14.7968	48.5313
4	1.0058	-0.1232	-0.7134	1.3493	1.9455	0.7407	0.0864	0.0706	-0.2022	0.4997	-0.2445	0.1829	0.2161	-0.2265	0.15	0.3493	-0.0879	-0.0084	0.2148	-0.0419	0.2687	-21.1193	-26.1202	37.3341
5	1.3635	-1.1484	-0.5654	0.9401	0.9861	0.3612	-0.1897	0.5568	0.1383	-0.0938	-0.0649	-0.6548	0.0969	-0.3889	0.1478	0.4853	-0.1618	0.0636	0.3684	0.0047	0.5128	-32.4898	-20.8495	56.6506
6	1.1857	0.8665	0.0652	2.3646	0.84	0.3967	-0.1834	0.3167	-0.0122	-0.4972	0.444	-0.2436	-0.3572	0.3645	-0.164	0.3516	-0.1041	0.014	0.2923	-0.0619	0.3016	5.8013	-8.7089	45.0651
7	0.6428	0.4569	0.286	1.3869	0.635	0.8371	0.1486	0.0413	0.267	-0.2925	0.1019	-0.1642	-0.4625	0.0921	-0.2153	0.4104	-0.1159	0.1282	0.2086	-0.0464	0.2643	-4.5961	8.58	46.6739
8	6.0868	2.9067	5.8989	5.9262	3.5026	2.657	-0.5327	0.1143	1.3147	-0.0036	-0.4691	1.601	0.0457	-0.5651	0.7625	0.1769	-0.0693	0.1163	0.5251	-0.2429	0.3895	18.5509	-5.8588	45.3082
9	-0.0996	-0.6169	-0.4642	0.9479	1.2562	0.9226	-0.1872	-0.4698	0.4801	0.0729	0.6553	-0.504	-0.208	0.3252	-0.3532	0.4095	-0.2223	0.122	0.4387	-0.2663	0.4835	5.1619	12.3533	58.536
10	6.7295	-0.8756	1.1553	-0.2989	4.9943	1.9357	1.2246	-0.203	1.9766	0.133	0.2402	-0.0362	0.9087	-0.5418	-0.9365	0.5115	-0.0845	-0.0201	0.3761	-0.0857	0.5498	18.6741	4.2616	46.7992
11	2.4383	0.1855	0.6268	2.2499	1.6731	5.6683	0.12	0.4229	0.2039	-0.6002	0.2816	0.1401	-0.4669	1.4349	-0.2908	0.3229	0.1056	0.0522	0.6037	0.039	0.3085	-14.7785	-22.6525	-4.0209
12	0.6394	-1.1787	-0.2025	1.3216	-1.5084	-0.6419	0.2169	0.3937	0.0049	-0.7051	-0.5325	-0.371	-0.1417	0.6465	0.2714	0.5165	0.1566	0.0822	0.58	0.0558	0.2885	-9.9193	-29.1586	-7.818
13	2.308	0.0918	-0.2187	0.2386	1.1075	0.9492	-0.1039	-0.0829	-0.2867	-0.4676	-0.3232	-0.3106	-0.3187	1.5018	0.4052	0.5362	0.2791	0.2694	1.3444	0.3799	0.5223	10.7462	-34.7901	-7.5337
14	0.9674	0.1325	-1.9369	1.471	-0.5085	2.8224	0.0631	0.2332	-0.0195	-0.6921	-0.5936	-0.3755	0.3517	0.9364	0.2439	0.4379	0.3275	0.1007	0.5909	0.0884	0.2189	-3.4131	-38.0559	-8.7443
15	5.1446	-0.9318	-3.4225	1.7149	-1.7466	-3.6746	-0.0457	1.3109	-0.5741	-0.9736	-0.539	-0.2661	0.7256	-0.4302	0.3723	0.5212	0.0331	0.2187	0.7346	0.3336	0.2365	-4.434	-18.166	-17.6791
16	1.8419	-0.521	-1.089	0.5977	-0.6924	1.1054	-0.1446	0.0161	-0.3284	-0.0452	0.1304	0.3087	0.66	0.4625	0.066	0.4919	0.1949	-0.0816	0.4188	-0.096	0.3922	-20.7122	-49.673	3.9742
17	-0.236	-0.0192	-1.3171	1.6189	-1.212	2.0939	-0.0994	-0.0011	-0.2922	0.0201	-0.2676	-0.0281	0.0928	0.2103	0.3333	0.138	0.0079	-0.012	0.2389	0.0422	0.2832	-13.2238	-44.2959	23.7105
18	0.0161	-0.5535	0.4768	1.9118	-1.0816	3.0509	0.1005	-0.0372	-0.0331	-0.1091	-0.5985	-0.4834	-0.0063	1.288	0.4905	0.1121	0.0784	0.0211	0.5352	0.2096	0.3518	-0.2366	-38.9522	15.4352
19	-0.0219	-1.1366	-0.6387	0.8236	-0.5226	2.1866	-0.0655	0.2167	-0.1624	-0.0351	-0.1016	0.0127	0.1878	0.3059	0.1486	0.1914	0.0593	-0.0158	0.2763	-0.0131	0.2821	-15.0263	-41.5066	13.3704
20	0.4844	2.1603	0.2387	2.4444	0.4818	1.9866	0.0104	0.171	-0.2098	0.2617	-0.1574	-0.0362	0.1868	0.0263	0.1559	0.133	0.0228	0.0046	0.1563	-0.0939	0.2913	-21.3142	-40.8737	24.1303
21	1.9429	0.6102	0.0671	1.4736	-0.0689	1.6695	0.0007	-0.23	-0.1642	0.7615	-0.15	0.2037	0.6925	-0.0855	0.1383	0.6526	-0.0944	0.0221	0.2545	-0.0379	0.2582	-50.5165	-14.137	1.5482
22	1.5262	-0.8476	-1.374	0.2343	-2.0521	2.6819	-0.3895	-0.4691	-1.6857	0.544	-0.926	-0.3546	0.0309	0.3399	1.1372	0.4456	-0.3362	0.2372	0.8419	-0.1063	1.0386	-66.8371	-4.0164	0.6689
23	0.61	-0.3644	-0.134	1.913	-1.4471	3.4158	-0.2681	-0.0224	-0.3941	-0.161	-0.6152	-0.1931	0.3537	0.2916	0.5778	0.2567	-0.0187	-0.0889	0.2728	0.0031	0.3407	-55.8662	1.9919	-10.5196
24	1.3772	-0.6567	0.8619	3.1755	1.1097	-0.3485	0.1527	0.1835	-0.1106	0.2621	-0.1557	0.231	0.442	-0.0165	0.0133	0.4348	0.0046	-0.0442	0.2668	0.0288	0.1899	-44.9094	-7.6961	-6.0066
25	1.4641	0.5668	0.2549	1.3288	1.477	2.8946	0.1865	0.1669	-0.3627	0.5901	-0.3283	0.2757	1.3048	-0.012	0.1158	0.9695	-0.0821	-0.0154	0.1903	-0.0457	0.3042	-50.6151	-24.1054	-5.3465
26	1.4969	-1.4945	1.2119	1.7718	-1.1452	8.3958	-1.0368	-0.0255	-0.1704	0.263	-0.6224	-0.1955	0.2056	1.3699	0.8861	0.4344	0.1355	0.024	0.6458	0.1713	0.4809	-19.4521	-7.0728	0.0902
27	1.449	-1.0357	-0.1948	1.8236	-0.5462	1.5268	0.0314	0.2106	0.512	0.2251	-0.2806	-0.6678	0.1204	0.627	0.2603	0.294	-0.1113	-0.1596	0.4304	0.1397	0.4596	-25.6615	8.8364	-2.0537
28	0.8879	0.3418	-0.067	3.133	-1.3042	2.0805	-0.2477	0.1339	0.3037	-0.0685	0.0594	-0.7581	-0.0625	-0.2497	0.1485	0.309	-0.0221	-0.0053	0.3153	0.1546	0.4641	-36.8945	16.6117	-8.961
29	0.2358	-0.2754	0.9817	3.3335	0.0434	0.9333	-0.0136	0.0455	0.2027	0.5937	-0.1113	-0.2565	0.0483	0.1138	0.122	0.3714	-0.0112	-0.0798	0.3108	0.0547	0.2452	-37.4191	6.5483	3.0843
30	-0.1159	0.8366	0.1022	1.6361	-0.0933	1.8479	-0.2393	0.013	0.4886	0.3459	0.1388	-0.8295	0.1235	0.9565	0.1637	0.4005	-0.0413	-0.2784	0.72	0.0534	0.6926	-19.2072	9.0581	5.0684
31	1.4306	0.6636	-2.5604	2.1472	-1.08	3.1964	-0.0012	-0.3358	-0.314	-0.0979	-0.3105	-0.4964	-0.2299	0.7883	0.3145	0.1207	-0.0146	-0.0035	0.4554	0.0079	0.3477	28.8237	-26.5624	38.0201
32	-0.0417	-0.2744	-3.0435	1.3714	-0.3651	4.3922	-0.1844	-1.2233	-0.3926	-0.1766	-0.7674	-0.7227	0.4252	1.7336	0.8905	0.0778	0.2143	0.08	0.8318	0.4761	0.9129	39.4291	-41.3803	42.7719
33	-0.9392	-0.3293	-2.2679	1.5624	-1.7913	4.8361	-0.356	-1.1142	-0.7408	0.6061	-0.8324	-0.4696	0.2428	1.7113	1.3485	0.1494	0.053	0.0215	0.8482	0.2395	0.6954	34.1335	-37.3162	46.7232
34	1.3931	0.3582	-2.3968	0.8716	-0.6837	2.1866	-0.3285	-0.0749	-0.4714	-0.0255	-0.0574	-0.5958	0.1419	0.5088	0.365	0.2386	0.0006	0.0431	0.3648	0.0274	0.4763	27.2066	-33.0999	38.5349
35	1.7099	0.7663	-1.6982	2.4569	0.0417	2.6622	0.0014	0.3285	-0.3375	-0.712	-0.4222	-0.3141	-0.2812	0.066	0.3181	0.3326	0.0786	0.0951	0.4824	-0.0173	0.4355	29.8369	-29.2934	26.4629
36	2.6221	1.542	-0.983	0.9473	1.107	4.8322	-0.3905	0.1721	-0.4862	0.311	-0.1342	-0.1694	0.8704	-0.6505	0.4563	0.3584	0.0095	0.0621	0.4628	-0.0751	0.496	9.8872	-43.7991	48.4563
37	-1.1867	-0.4036	-1.1171	0.9312	-0.4237	4.8895	-0.1419	-0.4898	-0.2296	0.3063	-0.4899	-0.2555	0.1199	1.2556	0.567	0.2437	-0.0382	-0.1277	0.7574	0.3027	0.5509	25.0266	-41.7274	66.4161
38	-2.1452	-1.8312	-1.133	-0.4989	-0.376	2.23	-0.1084	-0.1813	0.8459	0.0009	-0.1961	-0.6527	0.8601	1.3037	0.5403	0.2026	0.24	0.0625	0.6536	0.4152	0.8878	30.586	-45.6919	56.5386
39	1.2839	0.8088	-2.5332	0.2912	-1.5656	3.9412	-0.0448	-0.4257	-0.6511	0.3475	-0.529	-0.4766	-0.0794	0.3762	0.5193	0.2517	-0.0671	-0.0914	0.4056	0.056	0.4352	17.7062	-36.877	58.5652
40	1.014	-0.3897	-2.2202	1.6694	-1.2538	3.567	-0.2009	-0.2656	-0.1985	0.5046	-0.4884	0.2015	-0.4674	0.0719	0.5858	0.3502	-0.0906	-0.0548	0.5356	-0.0146	0.3687	9.8184	-36.5922	69.7009

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 1:80)	A	1 - 80
2	X-RAY DIFFRACTION	2	(chain A and resid 81:158)	A	81 - 158
3	X-RAY DIFFRACTION	3	(chain A and resid 159:222)	A	159 - 222
4	X-RAY DIFFRACTION	4	(chain A and resid 223:254)	A	223 - 254
5	X-RAY DIFFRACTION	5	(chain A and resid 255:261)	A	255 - 261
6	X-RAY DIFFRACTION	6	(chain B and resid 1:35)	B	1 - 35
7	X-RAY DIFFRACTION	7	(chain B and resid 36:212)	B	36 - 212
8	X-RAY DIFFRACTION	8	(chain B and resid 213:217)	B	213 - 217
9	X-RAY DIFFRACTION	9	(chain B and resid 218:253)	B	218 - 253
10	X-RAY DIFFRACTION	10	(chain B and resid 254:261)	B	254 - 261
11	X-RAY DIFFRACTION	11	(chain C and resid 1:20)	C	1 - 20
12	X-RAY DIFFRACTION	12	(chain C and resid 21:49)	C	21 - 49
13	X-RAY DIFFRACTION	13	(chain C and resid 50:109)	C	50 - 109
14	X-RAY DIFFRACTION	14	(chain C and resid 110:253)	C	110 - 253
15	X-RAY DIFFRACTION	15	(chain C and resid 254:261)	C	254 - 261
16	X-RAY DIFFRACTION	16	(chain D and resid 1:33)	D	1 - 33
17	X-RAY DIFFRACTION	17	(chain D and resid 34:81)	D	34 - 81
18	X-RAY DIFFRACTION	18	(chain D and resid 82:158)	D	82 - 158
19	X-RAY DIFFRACTION	19	(chain D and resid 159:216)	D	159 - 216
20	X-RAY DIFFRACTION	20	(chain D and resid 217:263)	D	217 - 263
21	X-RAY DIFFRACTION	21	(chain E and resid 1:80)	E	1 - 80
22	X-RAY DIFFRACTION	22	(chain E and resid 81:86)	E	81 - 86
23	X-RAY DIFFRACTION	23	(chain E and resid 87:106)	E	87 - 106
24	X-RAY DIFFRACTION	24	(chain E and resid 107:216)	E	107 - 216
25	X-RAY DIFFRACTION	25	(chain E and resid 217:260)	E	217 - 260
26	X-RAY DIFFRACTION	26	(chain F and resid 1:14)	F	1 - 14
27	X-RAY DIFFRACTION	27	(chain F and resid 15:80)	F	15 - 80
28	X-RAY DIFFRACTION	28	(chain F and resid 81:104)	F	81 - 104
29	X-RAY DIFFRACTION	29	(chain F and resid 105:207)	F	105 - 207
30	X-RAY DIFFRACTION	30	(chain F and resid 208:261)	F	208 - 261
31	X-RAY DIFFRACTION	31	(chain G and resid 1:69)	G	1 - 69
32	X-RAY DIFFRACTION	32	(chain G and resid 70:137)	G	70 - 137
33	X-RAY DIFFRACTION	33	(chain G and resid 138:154)	G	138 - 154
34	X-RAY DIFFRACTION	34	(chain G and resid 155:213)	G	155 - 213
35	X-RAY DIFFRACTION	35	(chain G and resid 214:260)	G	214 - 260
36	X-RAY DIFFRACTION	36	(chain H and resid 1:35)	H	1 - 35
37	X-RAY DIFFRACTION	37	(chain H and resid 36:127)	H	36 - 127
38	X-RAY DIFFRACTION	38	(chain H and resid 128:149)	H	128 - 149
39	X-RAY DIFFRACTION	39	(chain H and resid 150:216)	H	150 - 216
40	X-RAY DIFFRACTION	40	(chain H and resid 217:259)	H	217 - 259

-
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://pdbjlvh1.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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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