PDB-6qxs: Crystal structure of Enteroccocus faecalis thymidylate synthase (...

ID or keywords:

Entry

Database: PDB / ID: 6qxs

Title

Crystal structure of Enteroccocus faecalis thymidylate synthase (EfTS) in complex with FdUMP

Components

(Thymidylate synthase

) x 2

Keywords

TRANSFERASE / Enteroccocus faecalis thymidylate synthase / EfTS /

folate pathway /

inhibitor /

FdUMP

Function / homology

Function and homology information

thymidylate synthase /

thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process /

methylation /

cytoplasm
Similarity search - Function

Biological species

Enterococcus faecalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.88 Å

Authors

Pozzi, C. / Mangani, M.

Funding support

1items

Citation

Journal: Molecules / Year: 2019
Title: Structural Comparison ofEnterococcus faecalisand Human Thymidylate Synthase Complexes with the Substrate dUMP and Its Analogue FdUMP Provides Hints about Enzyme Conformational Variabilities.
Authors: Pozzi, C. / Ferrari, S. / Luciani, R. / Tassone, G. / Costi, M.P. / Mangani, S.

History

Deposition	Mar 7, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 10, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jul 10, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0	Nov 20, 2019	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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

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Related structure data

Related structure data	6qxgC 6qxhC 6qyaC 3uwlS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3uwl-1 1vza-1 6qya-2 1vzd-1 1thy-1 3bz0-1 5j7w-1 1tda-1 1nje-1 1tdb-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Thymidylate synthase

B: Thymidylate synthase

C: Thymidylate synthase

D: Thymidylate synthase

hetero molecules

147 kDa, 4 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
Evidence: gel filtration
73.7 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
73.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.040, 94.840, 97.000
Angle α, β, γ (deg.)	90.00, 94.01, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 2 types, 4 molecules ABCD

#1: Protein	Thymidylate synthase / / TSase Mass: 36462.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria) Strain: ATCC 700802 / V583 / Gene: thyA, EF_1576 / Production host: Escherichia coli (E. coli) / References: UniProt: Q834R3, thymidylate synthase
#2: Protein	Thymidylate synthase / / TSase Mass: 36385.977 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: thyA, EF_1576 / Production host: Escherichia coli (E. coli) / References: UniProt: Q834R3, thymidylate synthase

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Non-polymers , 4 types, 333 molecules

#3: Chemical	ChemComp-UFP / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Fluorodeoxyuridylate Type: DNA linking / Mass: 326.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₂FN₂O₈P / Comment: inhibitor*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-FFO / N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid / [6S]-5-FORMYL-TETRAHYDROFOLATE / 6S-FOLINIC ACID Mass: 473.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₃N₇O₇
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.81 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.2-2.5 M ammonium sulfate and 0.1 M HEPES, pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2017
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96861 Å / Relative weight: 1
Reflection	Resolution: 2.88→96.76 Å / Num. obs: 28081 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / B_iso Wilson estimate: 30.71 Å² / CC_1/2: 0.956 / R_merge(I) obs: 0.154 / R_pim(I) all: 0.123 / R_rim(I) all: 0.198 / Net I/σ(I): 4.2
Reflection shell	Resolution: 2.88→3.04 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.362 / Mean I/σ(I) obs: 2 / Num. unique obs: 4058 / CC_1/2: 0.845 / R_pim(I) all: 0.289 / R_rim(I) all: 0.466 / % possible all: 94.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3UWL

3uwl

Resolution: 2.88→96.76 Å / Cor.coef. F_o:F_c: 0.922 / Cor.coef. F_o:F_c free: 0.867 / SU B: 40.085 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.463

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25169	1350	4.8 %	RANDOM
R_work	0.19992	-	-	-
obs	0.20251	26635	94.42 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 38.774 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	-0.16 Å²
2-	-	0.11 Å²	0 Å²
3-	-	-	-0.08 Å²

Refine analyze

Luzzati coordinate error obs: 0.344 Å

Refinement step

Cycle: LAST / Resolution: 2.88→96.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9670	0	120	327	10117

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	10064
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.613	1.64	13681
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.833	5	1208
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.557	22.724	547
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.12	15	1553
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.351	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.13	0.2	1263
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	7910
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.774	2.218	4856
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.043	3.318	6056
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.895	2.294	5208
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	6.942	28.614	15014
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.88→2.955 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.296	119	-
R_work	0.291	1942	-
obs	-	-	95.2 %

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	2.4482	-3.963	-0.4945	6.8927	1.9206	2.735	0.2127	-0.0868	-0.0913	-0.4359	0.2265	-0.0327	-0.2275	0.2274	-0.4392	0.1453	-0.0333	-0.006	0.1203	-0.0354	0.2062	16.4282	4.8323	9.0033
2	3.0768	3.0805	3.2366	9.6736	-0.2312	5.2354	-0.1411	-0.025	-0.1022	-0.1367	0.2037	-0.165	-0.1585	-0.1531	-0.0626	0.1041	0.0269	0.0273	0.1179	-0.0405	0.1837	20.0377	-12.1482	7.0328
3	0.2614	0.0029	0.1761	0.1328	0.0534	0.1395	-0.1358	0.1335	-0.1126	0.0599	0.1289	0.1906	-0.0798	0.1345	0.0069	0.198	0.0085	0.1074	0.1975	0.1094	0.3444	19.889	-0.8029	15.2242
4	1.0462	-0.147	-0.6395	0.8172	1.962	4.7945	-0.4738	-0.1448	0.1227	-0.168	-0.0738	0.2585	-0.2672	-0.1475	0.5475	0.2914	0.1176	-0.0996	0.1266	0.0763	0.2821	6.8052	7.5012	22.9783
5	0.6333	-1.6183	0.199	5.72	-0.4571	0.0642	-0.0979	0.1501	-0.0202	0.2755	0.1121	-0.208	-0.0278	0.0639	-0.0142	0.1353	0.005	0.0054	0.2424	-0.0099	0.1599	10.3918	-0.7584	35.3728
6	1.9549	-2.1616	1.8312	3.446	-2.7569	2.2233	0.3221	0.0481	-0.183	0.028	-0.0981	0.2937	0.0359	0.0854	-0.224	0.1934	-0.0001	0.0322	0.2599	0.0249	0.1913	5.831	-5.5936	38.5961
7	4.3791	0.0741	-1.3326	0.3385	0.127	0.5089	-0.1159	0.2919	-0.6093	0.0108	0.0201	-0.1442	-0.0505	-0.0817	0.0957	0.2618	0.0053	0.0568	0.0778	-0.0434	0.1925	6.1654	-18.1304	33.9708
8	2.164	1.4518	0.8612	1.3846	0.6914	0.3868	0.4049	-0.0374	0.117	0.1306	-0.3944	0.0616	0.1514	-0.1162	-0.0105	0.2555	0.1377	-0.0591	0.3364	0.0186	0.2408	-0.5397	-25.8894	36.6333
9	4.8833	-3.874	1.1531	4.1052	1.5587	6.2135	0.0473	-0.0915	-0.1743	0.0786	-0.0387	0.1278	0.2832	-0.2873	-0.0085	0.0278	-0.0376	-0.0249	0.138	0.0829	0.2947	-1.1672	-15.0777	41.7625
10	0.3529	-0.6706	0.293	3.4524	-4.5532	7.5772	0.0014	-0.2241	0.0062	-0.137	0.1369	0.0723	0.2547	0.3438	-0.1384	0.0766	-0.0355	-0.013	0.2257	0.0157	0.2145	12.5262	-13.6725	39.6794
11	0.0962	-0.1907	-0.562	0.3796	1.1126	3.3896	-0.0184	0.0397	0.0106	0.0444	-0.0903	-0.0274	0.154	-0.2392	0.1087	0.0818	-0.0085	0.0229	0.1943	0.0069	0.2873	25.6816	-3.579	42.286
12	0.1599	-0.3157	0.0882	0.6542	-0.1773	0.0514	-0.051	-0.0311	-0.0389	0.1552	0.0648	0.0169	-0.0383	0.0042	-0.0137	0.1906	-0.0234	0.0291	0.1963	-0.0092	0.246	28.877	-1.3168	34.7762
13	0.2502	-0.4904	-0.4864	4.4966	0.6825	0.9695	0.0018	-0.0328	0.0223	-0.0573	0.0666	0.2245	-0.032	0.0682	-0.0684	0.2202	-0.0107	0.0289	0.1544	0.047	0.1623	23.8525	-0.4151	29.1053
14	0.2728	-0.5379	-0.1183	1.2585	0.8018	1.8305	0.0786	-0.0873	-0.0691	-0.1744	0.1726	-0.0018	-0.1692	-0.067	-0.2512	0.1239	-0.0182	0.0243	0.2106	-0.0054	0.2192	19.5811	3.5906	23.7842
15	3.6113	1.1752	0.6911	2.2768	2.9052	3.9259	-0.4516	-0.2043	-0.0248	0.0411	0.1615	0.2163	0.1789	0.3077	0.29	0.2222	0.0366	-0.0001	0.1633	0.005	0.1703	15.6846	8.0003	31.6752
16	1.009	1.2319	1.7929	1.6309	2.0133	3.533	-0.0745	-0.1262	0.1006	-0.1465	-0.1157	0.1441	-0.1548	-0.3664	0.1902	0.1572	0.0064	0.0166	0.2107	-0.0352	0.2117	18.9453	3.854	22.4857
17	6.2016	-2.7576	3.2941	1.7398	-2.5372	8.9009	-0.0317	0.2281	-0.0151	0.0437	0.082	0.0791	0.0071	-0.1546	-0.0503	0.1131	-0.0109	0.0041	0.1354	0.0072	0.1429	6.5927	-1.8693	7.3833
18	0.6116	0.671	0.5013	6.5253	5.6167	4.8551	-0.1	0.01	0.1266	-0.4788	-0.0023	0.1486	-0.4483	-0.0151	0.1022	0.2435	0.0262	-0.0133	0.0986	0.0574	0.1451	6.119	12.0439	14.1558
19	5.5332	2.7764	0.3506	1.4007	0.1651	0.0396	0.1807	-0.4102	0.1076	0.0593	-0.2036	0.0575	0.057	-0.0158	0.0228	0.1377	0.043	0.0301	0.251	-0.02	0.1384	8.6825	10.9708	41.0549
20	3.1494	-1.3037	-0.2167	0.6099	0.2371	0.3261	0.0165	0.145	-0.0514	0.0537	-0.2713	0.1376	0.11	-0.4553	0.2548	0.1844	-0.1689	0.0376	0.6683	-0.3238	0.2715	2.112	6.9075	22.2388
21	1.8334	-1.6054	-0.9507	2.3446	3.0693	5.8257	0.0997	0.3346	0.2533	0.0011	-0.2486	-0.1063	0.1347	-0.0725	0.149	0.1144	-0.0513	0.0312	0.2389	0.0099	0.1696	39.323	13.2601	12.8394
22	0.4439	-0.7859	0.8722	2.7054	-0.7041	4.6762	-0.1234	-0.1053	0.0375	-0.0338	0.0741	0.1541	-0.1326	-0.0555	0.0493	0.1618	0.0407	-0.0319	0.1586	0.008	0.1627	36.6368	20.5291	26.4367
23	0.4974	0.3556	-0.0014	0.591	0.0295	0.0212	0.0038	0.0007	0.0036	-0.0222	-0.0484	0.0214	0.0207	0.0352	0.0446	0.1544	-0.0156	0.0293	0.2486	0.0147	0.1647	43.7549	5.445	17.6239
24	1.0123	0.5479	0.5424	2.7941	1.5752	0.9509	0.0681	0.0396	-0.0574	0.2909	-0.0383	-0.0895	0.1751	-0.0202	-0.0299	0.1589	-0.0058	0.0615	0.2084	0.0183	0.1922	54.0779	-6.3931	28.7414
25	2.478	1.3068	1.2655	0.8123	1.3424	4.3789	-0.0005	-0.1791	0.0622	0.0095	-0.0954	0.0408	0.0988	-0.1441	0.0959	0.2178	-0.0031	-0.0017	0.1624	0.0345	0.1449	52.8212	3.5987	37.7026
26	0.1781	0.6079	0.3106	2.2119	1.6432	3.0412	0.0184	-0.0373	-0.0536	0.0675	-0.0965	-0.1481	0.0267	0.0477	0.0781	0.0987	-0.019	-0.0092	0.1818	0.0181	0.1696	58.0514	5.8633	47.1128
27	6.0992	-1.4589	-0.8231	7.722	3.2421	1.3829	0.0813	0.2503	0.3678	-0.0105	-0.0285	-0.0322	0.0089	-0.0616	-0.0528	0.1403	-0.0335	-0.0103	0.1658	0.0389	0.1505	55.8839	17.1024	37.4753
28	9.1801	-3.9554	-2.6822	6.4781	-2.1934	3.1336	-0.2601	0.081	0.3884	0.4721	0.0609	-0.6164	-0.1772	-0.0835	0.1991	0.0961	-0.0903	-0.0307	0.1939	-0.021	0.1906	64.1771	12.9405	38.3622
29	1.7906	-0.324	-2.3944	0.0989	0.745	6.1542	0.0221	0.1479	-0.1143	0.016	0.021	-0.0364	0.0591	0.0155	-0.0431	0.0735	-0.0008	-0.0523	0.1859	-0.0573	0.2389	62.1222	-3.9693	39.0015
30	0.4975	1.2094	-0.1577	2.993	-0.3911	0.0517	0.1124	-0.0581	0.0343	0.1662	-0.1092	0.0577	-0.0236	0.0051	-0.0032	0.2193	-0.012	0.0462	0.1612	-0.0111	0.208	43.2587	-9.579	34.5789
31	0.084	-0.0348	0.6738	0.2974	-0.1223	6.5307	-0.0242	-0.0191	0.0185	-0.0318	-0.0909	-0.0263	0.1485	-0.1313	0.1151	0.1546	0.0129	0.0109	0.1488	-0.0068	0.1618	35.7149	-17.9909	28.0151
32	0.6208	-0.3746	-0.3299	0.2276	0.2004	0.1792	-0.0664	-0.0026	-0.1631	0.0425	-0.02	0.0903	0.0285	-0.0245	0.0863	0.1918	-0.0527	-0.0015	0.1963	-0.0388	0.2234	31.6468	-10.3455	27.0438
33	2.6813	1.1298	4.5072	1.9434	0.7304	8.6983	0.0447	0.1216	-0.1301	0.4217	0.0544	-0.0155	-0.335	0.0746	-0.0991	0.1831	0.0355	-0.039	0.1789	-0.0446	0.1971	39.3148	-0.47	31.4476
34	0.1944	0.1045	-0.1215	0.1639	-0.0849	0.0872	0.0959	-0.0044	-0.006	0.0474	-0.063	0.0742	-0.0397	0.0273	-0.0329	0.1853	0.0264	0.0172	0.1903	-0.0254	0.2282	38.9286	-2.8646	17.3884
35	4.3524	-5.5283	2.0663	7.0245	-2.625	0.9829	0.0519	0.1508	0.251	-0.0539	-0.188	-0.3379	0.0357	0.0658	0.1361	0.1563	0.0097	0.0146	0.1508	-0.039	0.2184	38.5936	-14.1072	8.9169
36	1.4663	2.6112	0.9155	5.047	1.7949	0.6399	-0.1491	-0.0389	0.0296	-0.4591	0.148	0.0066	-0.1713	0.0679	0.0011	0.2578	-0.022	-0.0076	0.1794	0.0067	0.1695	37.0445	7.1472	20.8598
37	2.0956	-2.6273	-2.5478	4.067	3.3122	3.1248	0.1004	-0.104	-0.0243	-0.0572	-0.1203	-0.1514	-0.1399	0.0815	0.0199	0.1329	-0.0574	-0.0203	0.2053	0.007	0.1551	48.3466	18.9616	16.6746
38	0.6716	0.9729	0.221	1.677	0.5326	0.2535	-0.0801	0.1645	-0.1603	-0.0634	0.184	-0.3423	0.0531	0.024	-0.104	0.1727	0.0211	0.0791	0.1837	-0.0422	0.2218	49.1825	-8.9301	10.0359
39	1.9099	-0.6692	-0.2992	0.6854	-1.5848	6.4028	-0.0128	0.0984	-0.1311	0.0527	-0.0811	0.0161	-0.1666	0.207	0.094	0.114	0.0111	0.0136	0.1821	-0.0164	0.1362	54.7388	-10.0128	13.2487
40	1.4148	0.2216	0.2083	0.0433	0.0361	0.0325	-0.0656	0.0231	0.1511	-0.0271	0.0271	0.0477	-0.0121	0.0092	0.0384	0.1771	-0.0079	-0.0008	0.156	0.0029	0.1789	53.8026	10.3632	16.9676
41	2.7662	2.9325	-1.0634	3.1602	-1.1971	0.565	0.0598	0.1046	0.0502	0.1173	0.1989	0.1388	-0.0738	-0.0802	-0.2587	0.0832	0.0791	0.0493	0.3367	-0.0061	0.3602	15.397	-44.7329	37.3443
42	1.633	-0.4058	-0.4544	0.7411	0.283	0.199	-0.0925	-0.0408	-0.0936	0.0719	0.1429	0.0013	0.0283	0.0002	-0.0504	0.1572	-0.0112	-0.007	0.1818	0.0954	0.1808	13.8988	-47.5138	27.7651
43	0.0601	0.0573	0.0566	0.0563	0.0556	0.0549	-0.0651	0.033	-0.0217	-0.078	0.0546	-0.0004	-0.0772	0.0413	0.0105	0.1359	-0.0179	-0.0313	0.2333	0.1226	0.2487	10.5256	-41.4781	7.6326
44	4.9556	2.5395	1.545	2.7389	4.586	10.5087	-0.0167	-0.1317	0.1307	-0.1172	0.0264	0.0657	-0.2746	0.1968	-0.0097	0.1682	0.0286	-0.052	0.1044	0.0412	0.1864	5.2838	-38.257	11.039
45	1.036	1.6932	2.1105	3.2422	3.8628	4.7158	0.0331	0.1602	0.0325	0.3325	0.0515	0.0147	0.3571	0.1943	-0.0846	0.214	-0.0516	-0.0924	0.2044	-0.0361	0.2943	6.9598	-24.5856	9.8214
46	0.058	-0.2294	0.2247	7.1877	-8.0609	9.067	-0.0267	0.0902	0.0257	0.1318	-0.203	-0.1886	-0.1506	0.1535	0.2298	0.1158	0.025	-0.0485	0.212	-0.0635	0.2487	1.7058	-18.0357	6.9177
47	17.9518	5.6811	-8.3908	1.8014	-2.6554	3.922	0.2299	-0.2381	0.2749	0.0625	-0.0957	0.0908	-0.1061	0.1101	-0.1342	0.0622	0.0326	-0.1038	0.1381	0.0573	0.344	0.1203	-28.8436	5.1064
48	0.1273	-0.0346	-0.9953	0.024	0.298	8.7534	0.0538	-0.0154	-0.0103	0.0014	0.0593	0.0169	-0.0314	0.1589	-0.113	0.1739	0.0241	-0.1036	0.2051	0.0912	0.2947	5.4635	-29.502	-2.1096
49	1.7646	1.4218	-1.5367	1.146	-1.2354	1.3815	-0.0043	-0.1112	-0.0075	-0.0005	-0.0865	0.0046	0.0603	0.1946	0.0908	0.0758	0.1369	0.0952	0.2689	0.1221	0.2785	15.8312	-31.9032	7.7858
50	7.3436	5.4958	-2.9625	4.7998	-1.5994	1.753	0.0565	0.1194	-0.1417	-0.0713	-0.098	-0.1259	-0.146	-0.21	0.0415	0.1839	0.0141	-0.0241	0.1421	0.0458	0.1395	27.9728	-36.5005	5.6348
51	1.2664	0.9632	0.1029	6.6613	-0.8752	0.1624	0.0404	-0.0169	0.0868	-0.0672	-0.1239	-0.37	0.0289	0.0125	0.0834	0.1836	-0.0275	0.045	0.1637	-0.0218	0.1868	28.9641	-47.4313	4.5627
52	0.7699	0.05	0.8109	0.0159	0.0578	0.8611	0.1175	-0.0371	0.001	-0.006	-0.0743	0.0079	0.1261	-0.0671	-0.0431	0.1073	0.0404	0.0533	0.2757	-0.0094	0.2245	31.6249	-43.6034	13.5116
53	2.7377	1.5199	0.7762	5.6358	2.9232	1.5164	-0.1303	-0.2286	0.0671	0.0667	0.0516	0.1665	0.0345	0.0374	0.0787	0.2415	-0.0081	0.1082	0.1812	0.0756	0.1142	22.6724	-36.4171	17.9551
54	0.8129	-0.1484	-0.797	7.7308	-1.7502	1.4744	-0.068	-0.1325	-0.1082	-0.3075	0.0747	0.082	0.1098	0.2123	-0.0067	0.1406	0.0132	0.0145	0.1455	-0.0176	0.1637	29.3448	-56.6467	16.1066
55	0.5806	-0.2185	-0.5085	2.4006	-1.0039	1.0631	0.2107	0.1113	0.2181	-0.3221	-0.0445	-0.1233	-0.0518	-0.1115	-0.1662	0.1375	0.0177	0.0221	0.2627	-0.0057	0.2081	18.3031	-46.8761	23.1959
56	4.7403	-0.0951	2.2915	0.0197	-0.0541	1.1115	0.1807	0.3635	-0.1282	0.0334	-0.0679	0.0694	0.0771	0.1917	-0.1128	0.1983	-0.0698	0.0979	0.2443	-0.0785	0.3377	17.2521	-52.7192	13.6916
57	0.5894	-0.7088	-0.041	1.9156	0.5489	0.4332	-0.006	-0.0326	0.0487	0.1379	0.1813	-0.0062	0.1888	0.0486	-0.1752	0.1863	-0.0202	-0.0402	0.1986	0.0206	0.2522	20.6887	-51.9102	20.2925
58	0.2303	-0.3993	-0.244	6.1805	3.5909	2.245	-0.0601	0.2183	0.1234	0.4018	0.0173	-0.0749	0.1318	-0.0546	0.0428	0.1217	-0.0127	-0.0376	0.2573	0.0735	0.2314	5.3118	-44.3956	36.0545
59	1.42	-0.8886	-1.1465	0.7209	1.1964	2.3547	-0.0322	0.4864	-0.1853	0.0496	-0.2505	0.1492	0.0364	-0.2568	0.2827	0.1111	-0.0734	-0.0354	0.3345	0.0302	0.1532	10.3781	-57.2338	9.1889
60	1.0724	-0.1011	-0.8632	0.0567	0.127	0.7589	0.0823	0.3844	-0.0001	-0.0472	-0.1316	0.0944	-0.0864	-0.462	0.0492	0.0606	0.0409	-0.1182	0.5202	-0.0601	0.2638	2.5276	-50.7642	20.6599
61	0.7718	-0.312	-0.0556	0.5113	1.6278	6.6969	0.0291	-0.1685	-0.1182	0.0533	0.1105	0.0156	0.2674	0.1999	-0.1396	0.1996	0.0258	-0.0111	0.1535	0.0157	0.1601	37.8821	-58.4294	35.7007
62	1.8241	2.7526	-1.0991	6.8696	-2.804	1.6338	0.0606	0.2646	-0.3221	0.3342	-0.1119	0.099	-0.5881	0.0934	0.0513	0.4416	-0.0524	-0.0327	0.2359	-0.0835	0.2499	36.4694	-64.9587	21.7592
63	0.9001	0.0141	-0.5916	1.9314	1.7514	1.9962	-0.1332	-0.0163	-0.0358	0.1075	-0.0146	0.1372	0.1874	-0.0231	0.1478	0.2089	0.0258	-0.019	0.163	0.0456	0.162	36.6791	-53.5267	29.3376
64	1.3095	0.706	0.1517	2.057	0.8078	0.3328	0.1005	0.0187	-0.0616	-0.024	-0.0313	-0.2065	-0.0255	-0.0307	-0.0692	0.1416	0.0038	-0.0301	0.2733	0.0204	0.1982	49.9046	-46.4879	35.5044
65	0.3045	-0.9649	-0.5924	3.398	2.0374	1.2282	0.0749	0.0343	-0.0119	-0.046	-0.0238	-0.1146	-0.0597	-0.0223	-0.0511	0.1776	-0.0033	-0.0354	0.2139	0.0091	0.1892	54.075	-38.2833	22.7369
66	0.3427	0.4021	-1.0392	1.6356	0.1954	4.9445	0.0492	0.0436	0.0275	0.1007	0.0077	0.1002	-0.171	-0.1275	-0.0569	0.1706	0.0043	0.0185	0.1548	0.0008	0.1449	55.9418	-47.8617	10.3742
67	0.8218	1.2856	-0.2828	2.5443	-2.3681	7.0731	0.2075	-0.1516	0.1398	0.3183	-0.2843	0.1925	-0.0729	0.1712	0.0769	0.1003	0.0478	0.0239	0.1935	-0.0103	0.2016	62.5454	-52.2043	4.6426
68	6.0583	-5.4418	-0.1329	10.0923	2.3224	0.9413	0.289	0.5057	-0.0508	-0.0503	-0.258	-0.034	0.092	0.1057	-0.031	0.1485	0.074	0.0507	0.2188	0.0558	0.1507	59.2699	-61.8659	13.8299
69	2.9169	1.1256	-0.01	9.6586	-5.0275	2.7381	0.0896	-0.2653	0.0197	-0.4277	-0.0349	0.1221	0.2544	-0.0166	-0.0547	0.0798	0.0449	-0.0053	0.2409	-0.0144	0.1347	65.6991	-54.6907	14.5839
70	2.2293	1.3378	1.8434	8.4854	5.3123	3.8278	-0.0637	0.1612	0.2545	-0.0355	0.0241	-0.1661	-0.0448	0.1031	0.0396	0.1149	0.0233	0.0249	0.2145	0.031	0.1561	65.7565	-42.0828	15.1331
71	1.1264	-2.4248	2.6742	5.31	-5.8241	6.4035	0.0588	-0.0138	0.0138	-0.2944	-0.0928	-0.0545	0.2741	0.0415	0.034	0.2804	0.1415	0.0994	0.2121	-0.0209	0.1354	58.8257	-37.6404	9.5271
72	2.5708	1.0613	0.1031	0.4391	0.0421	0.0045	0.0619	-0.0601	0.0554	0.0332	-0.0494	0.0286	-0.0041	0.0017	-0.0125	0.2657	0.0192	-0.0139	0.1649	-0.0022	0.1618	42.8983	-34.869	17.1485
73	0.0526	0.0764	-0.6153	0.6428	-0.9768	7.6657	0.0123	0.0117	-0.0027	0.0328	-0.0382	0.1043	-0.0425	0.1005	0.0259	0.1396	-0.0064	-0.0061	0.1526	-0.0132	0.1758	36.8796	-26.7845	19.0545
74	0.9647	0.5496	0.46	0.3142	0.2598	0.2267	-0.0711	0.0456	0.0776	-0.029	0.0347	0.039	-0.0593	-0.0134	0.0364	0.2062	0.0685	0.0112	0.1928	0.0061	0.1808	30.8468	-32.7728	23.2767
75	0.1843	0.5213	0.6717	2.8822	2.7343	3.097	0.002	0.0946	0.0429	0.2399	-0.1888	0.2013	0.3656	0.1524	0.1868	0.3607	0.0428	0.0291	0.239	0.0085	0.1365	39.9389	-43.0941	16.6348
76	0.009	0.0787	-0.0441	0.7712	-0.4182	0.2303	0.0049	0.0077	0.0087	0.0136	0.0012	-0.0104	-0.0037	-0.0241	-0.0061	0.1993	0.0048	0.0002	0.1859	-0.0156	0.2031	37.6573	-42.1704	31.7428
77	2.8095	1.3906	-0.5303	4.5522	2.6283	2.2766	0.0201	-0.2339	-0.05	-0.1403	0.1044	-0.2501	-0.0875	0.1711	-0.1245	0.2238	0.0176	-0.0096	0.1501	-0.0492	0.189	36.152	-34.3331	38.5138
78	2.3297	-1.4337	-0.283	1.7885	-1.2649	2.503	-0.3091	0.1535	-0.1065	0.3084	-0.0515	-0.0706	-0.061	0.1287	0.3605	0.1925	0.037	0.0081	0.2445	0.0528	0.2384	42.8154	-59.8594	27.318
79	0.1487	-0.2752	-0.2772	0.6315	0.7718	1.0701	-0.1022	-0.0616	0.0387	0.0923	0.0693	-0.0233	-0.0263	0.0511	0.0329	0.1749	0.0125	-0.0536	0.2273	0.0106	0.1783	48.4666	-39.6851	39.6785
80	2.2646	2.8528	2.6888	3.6255	3.408	3.2063	-0.2417	0.0911	0.02	-0.2726	0.1747	0.0876	-0.2715	0.1484	0.0671	0.2039	0.0498	0.0384	0.2194	0.025	0.1973	52.7669	-55.0414	33.5393

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 15
2	X-RAY DIFFRACTION	2	A	16 - 21
3	X-RAY DIFFRACTION	3	A	22 - 40
4	X-RAY DIFFRACTION	4	A	41 - 56
5	X-RAY DIFFRACTION	5	A	57 - 63
6	X-RAY DIFFRACTION	6	A	64 - 80
7	X-RAY DIFFRACTION	7	A	81 - 90
8	X-RAY DIFFRACTION	8	A	91 - 120
9	X-RAY DIFFRACTION	9	A	121 - 135
10	X-RAY DIFFRACTION	10	A	136 - 145
11	X-RAY DIFFRACTION	11	A	146 - 169
12	X-RAY DIFFRACTION	12	A	170 - 193
13	X-RAY DIFFRACTION	13	A	194 - 204
14	X-RAY DIFFRACTION	14	A	205 - 227
15	X-RAY DIFFRACTION	15	A	228 - 241
16	X-RAY DIFFRACTION	16	A	242 - 262
17	X-RAY DIFFRACTION	17	A	263 - 269
18	X-RAY DIFFRACTION	18	A	270 - 280
19	X-RAY DIFFRACTION	19	A	281 - 296
20	X-RAY DIFFRACTION	20	A	297 - 313
21	X-RAY DIFFRACTION	21	B	1 - 12
22	X-RAY DIFFRACTION	22	B	13 - 21
23	X-RAY DIFFRACTION	23	B	22 - 60
24	X-RAY DIFFRACTION	24	B	61 - 81
25	X-RAY DIFFRACTION	25	B	82 - 88
26	X-RAY DIFFRACTION	26	B	89 - 101
27	X-RAY DIFFRACTION	27	B	102 - 110
28	X-RAY DIFFRACTION	28	B	111 - 120
29	X-RAY DIFFRACTION	29	B	121 - 137
30	X-RAY DIFFRACTION	30	B	138 - 154
31	X-RAY DIFFRACTION	31	B	155 - 170
32	X-RAY DIFFRACTION	32	B	171 - 191
33	X-RAY DIFFRACTION	33	B	192 - 200
34	X-RAY DIFFRACTION	34	B	201 - 241
35	X-RAY DIFFRACTION	35	B	242 - 248
36	X-RAY DIFFRACTION	36	B	249 - 260
37	X-RAY DIFFRACTION	37	B	261 - 274
38	X-RAY DIFFRACTION	38	B	275 - 292
39	X-RAY DIFFRACTION	39	B	293 - 301
40	X-RAY DIFFRACTION	40	B	302 - 315
41	X-RAY DIFFRACTION	41	C	1 - 21
42	X-RAY DIFFRACTION	42	C	22 - 53
43	X-RAY DIFFRACTION	43	C	54 - 75
44	X-RAY DIFFRACTION	44	C	76 - 81
45	X-RAY DIFFRACTION	45	C	82 - 90
46	X-RAY DIFFRACTION	46	C	91 - 120
47	X-RAY DIFFRACTION	47	C	121 - 128
48	X-RAY DIFFRACTION	48	C	129 - 137
49	X-RAY DIFFRACTION	49	C	138 - 146
50	X-RAY DIFFRACTION	50	C	147 - 157
51	X-RAY DIFFRACTION	51	C	158 - 171
52	X-RAY DIFFRACTION	52	C	172 - 190
53	X-RAY DIFFRACTION	53	C	191 - 201
54	X-RAY DIFFRACTION	54	C	202 - 206
55	X-RAY DIFFRACTION	55	C	207 - 229
56	X-RAY DIFFRACTION	56	C	230 - 240
57	X-RAY DIFFRACTION	57	C	241 - 259
58	X-RAY DIFFRACTION	58	C	260 - 275
59	X-RAY DIFFRACTION	59	C	276 - 294
60	X-RAY DIFFRACTION	60	C	295 - 313
61	X-RAY DIFFRACTION	61	D	1 - 13
62	X-RAY DIFFRACTION	62	D	14 - 21
63	X-RAY DIFFRACTION	63	D	22 - 42
64	X-RAY DIFFRACTION	64	D	43 - 59
65	X-RAY DIFFRACTION	65	D	60 - 81
66	X-RAY DIFFRACTION	66	D	82 - 93
67	X-RAY DIFFRACTION	67	D	94 - 101
68	X-RAY DIFFRACTION	68	D	102 - 113
69	X-RAY DIFFRACTION	69	D	114 - 121
70	X-RAY DIFFRACTION	70	D	122 - 131
71	X-RAY DIFFRACTION	71	D	132 - 140
72	X-RAY DIFFRACTION	72	D	141 - 152
73	X-RAY DIFFRACTION	73	D	153 - 169
74	X-RAY DIFFRACTION	74	D	170 - 188
75	X-RAY DIFFRACTION	75	D	189 - 201
76	X-RAY DIFFRACTION	76	D	202 - 240
77	X-RAY DIFFRACTION	77	D	241 - 251
78	X-RAY DIFFRACTION	78	D	252 - 269
79	X-RAY DIFFRACTION	79	D	270 - 301
80	X-RAY DIFFRACTION	80	D	302 - 315

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News

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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

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