PDB-6qyq: Crystal structure of human thymidylate synthase (hTS) variant R175C

ID or keywords:

Entry

Database: PDB / ID: 6qyq

Title

Crystal structure of human thymidylate synthase (hTS) variant R175C

Components

(Thymidylate synthase

) x 4

Keywords

TRANSFERASE /

human thymidylate synthase /

folate pathway / R175C / interface variant

Function / homology

Function and homology information

uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / response to vitamin A /

thymidylate synthase / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Pozzi, C. / Mangani, M.

Funding support

1items

Citation

Journal: Molecules / Year: 2019
Title: Structural and Functional Characterization of the Human Thymidylate Synthase (hTS) Interface Variant R175C, New Perspectives for the Development of hTS Inhibitors.
Authors: Pozzi, C. / Ferrari, S. / Luciani, R. / Costi, M.P. / Mangani, S.

History

Deposition	Mar 9, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 17, 2019	Provider: repository / Type: Initial release
Revision 1.1	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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Download

PDBx/mmCIF format	6qyq.cif.gz	487.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6qyq.ent.gz	402 KB	Display	PDB format
PDBx/mmJSON format	6qyq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	1hvyS S: Starting model for refinement
Similar structure data	5noo-1 6qxg-1 6qxh-1 5x69-2 5noo-2 4e5o-2 3gg5-2 4o1x-2 3hb8-3 5x5d-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
Related items in Molecule of the Month	#233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #34 - Oct 2002 Dihydrofolate Reductase similarity (1)

Deposited unit

A: Thymidylate synthase

C: Thymidylate synthase

B: Thymidylate synthase

D: Thymidylate synthase

hetero molecules

151 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
75.5 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
75.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.490, 96.520, 139.080
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 4 types, 4 molecules ACBD

#1: Protein	Thymidylate synthase / / TSase Mass: 37252.613 Da / Num. of mol.: 1 / Mutation: R175C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS, OK/SW-cl.29 / Plasmid: pQE80L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04818, thymidylate synthase
#2: Protein	Thymidylate synthase / / TSase Mass: 37298.637 Da / Num. of mol.: 1 / Mutation: R175C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS, OK/SW-cl.29 / Plasmid: pQE80L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04818, thymidylate synthase
#3: Protein	Thymidylate synthase / / TSase Mass: 37298.703 Da / Num. of mol.: 1 / Mutation: R175C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS, OK/SW-cl.29 / Plasmid: pQE80L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04818, thymidylate synthase
#4: Protein	Thymidylate synthase / / TSase Mass: 37252.613 Da / Num. of mol.: 1 / Mutation: R175C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS, OK/SW-cl.29 / Plasmid: pQE80L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04818, thymidylate synthase

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Non-polymers , 4 types, 486 molecules

#5: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: 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
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.21 Å³/Da / Density % sol: 44.48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 25 % saturated ammonium sulfate, 20 mM beta-mercaptoethanol and 0.1 M TRIS, pH 8.3

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 2.25→38.35 Å / Num. obs: 57746 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / B_iso Wilson estimate: 39.99 Å² / R_merge(I) obs: 0.073 / R_pim(I) all: 0.043 / R_rim(I) all: 0.085 / Net I/σ(I): 10
Reflection shell	Resolution: 2.25→2.37 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.297 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 8475 / R_pim(I) all: 0.179 / R_rim(I) all: 0.349 / % 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: 1HVY

1hvy

Resolution: 2.25→36.7 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.924 / SU B: 14.456 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.248

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25072	2917	5.1 %	RANDOM
R_work	0.18326	-	-	-
obs	0.18662	54740	92.53 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 46.493 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.04 Å²	0 Å²	0 Å²
2-	-	-0.07 Å²	0 Å²
3-	-	-	0.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→36.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9146	0	102	474	9722

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	9484
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.848	1.638	12859
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.51	5	1144
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.502	21.811	508
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.399	15	1509
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.157	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.134	0.2	1186
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	7356
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	1.77	2.29	4600
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.906	3.416	5736
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.285	2.446	4884
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	7.136	30.308	13853
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: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.533	229	-
R_work	0.492	4019	-
obs	-	-	93.51 %

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	0.8252	0.0467	1.7754	0.1747	0.5035	4.961	0.1504	-0.2756	0.037	-0.035	0.1118	-0.0677	0.0906	-0.4345	-0.2622	0.2883	0.0111	0.0736	0.2743	0.0485	0.2392	-11.8728	2.0132	40.7344
2	9.2474	5.6195	2.96	3.4551	1.7698	0.9713	-0.0084	-0.1523	0.2327	-0.0418	-0.0095	0.2351	0.0484	-0.1168	0.0179	0.3441	-0.1208	-0.0507	0.2046	0.1451	0.2799	-17.5361	-4.0955	28.0982
3	0.3421	0.382	-0.3569	0.8852	-1.6469	3.7903	0.3294	0.299	-0.1396	0.066	0.1658	0.0844	0.4453	0.1861	-0.4953	0.5655	0.3343	-0.3081	0.4055	-0.1975	0.2195	-10.5577	-6.999	15.8183
4	0.2157	0.2862	-0.4771	0.7824	-0.6604	2.3517	0.1419	0.0194	-0.0344	0.3064	0.16	0.132	0.0746	-0.2753	-0.3018	0.3709	0.0108	-0.0241	0.1754	0.0508	0.2837	-8.822	6.9374	34.08
5	2.3343	2.3776	-1.6776	2.4763	-1.6194	2.6707	0.0157	0.0741	-0.195	0.1358	0.1231	-0.2347	-0.01	0.1131	-0.1388	0.3069	0.049	-0.0816	0.1747	-0.0453	0.2796	6.7851	4.2997	34.5461
6	0.4848	-0.9578	-0.1894	2.1084	0.0866	5.2632	0.0136	0.0562	-0.0008	0.0255	0.0258	-0.2081	0.1554	0.4196	-0.0394	0.1435	0.0642	-0.054	0.2358	-0.0874	0.3452	14.9675	4.454	25.2382
7	2.9008	0.0021	0.7377	0.0766	-0.8493	9.7066	-0.3021	0.1415	-0.0434	-0.0271	0.0156	-0.026	0.2709	0.0068	0.2866	0.2372	0.0077	-0.0076	0.2155	-0.0692	0.2406	12.3325	-0.4804	11.2227
8	1.4312	-0.6809	-1.2982	2.3116	1.789	2.7803	0.1728	0.1691	-0.0905	0.1022	0.1883	-0.1243	-0.2932	0.14	-0.3611	0.1905	-0.0247	0.0073	0.2493	-0.0796	0.2928	12.411	13.1401	16.0749
9	2.3701	0.4165	-3.1887	0.2184	-0.7547	4.5709	0.3159	0.0241	0.0931	0.1848	-0.1465	-0.028	-0.6547	0.1924	-0.1694	0.2506	-0.2002	0.1697	0.2045	-0.1262	0.4249	14.8395	21.5408	19.2778
10	1.0072	-0.0736	-0.3986	5.4352	3.0605	1.862	-0.0548	-0.0778	0.0447	-0.1493	0.1678	-0.1532	-0.1407	0.1253	-0.113	0.489	-0.0151	0.0471	0.0662	-0.0457	0.2629	2.4547	28.834	32.3533
11	0.4131	-1.7903	-0.4877	10.4535	1.083	1.4528	0.0621	0.1198	0.0612	0.2263	-0.1278	-0.1508	-0.1527	-0.0303	0.0657	0.2731	0.0661	0.0529	0.2948	0.0459	0.2729	-3.9577	26.4384	27.28
12	3.243	-3.5149	-2.5431	6.2011	5.9251	6.1953	0.111	0.1331	0.1871	-0.2818	0.0127	-0.171	-0.3164	0.095	-0.1237	0.2615	-0.0402	0.0752	0.3072	0.0628	0.2015	0.9002	16.6217	14.7887
13	3.4355	-6.1725	-3.8602	11.1302	7.0648	4.8766	0.0339	0.0004	-0.293	-0.0912	-0.0112	0.4118	-0.1434	-0.2258	-0.0227	0.1383	-0.0265	0.0607	0.3171	0.0143	0.357	5.6777	10.0393	12.2465
14	0.4818	0.8144	0.0973	1.4007	0.145	0.2375	0.0776	-0.022	-0.0609	0.0543	-0.0463	-0.0934	-0.0099	-0.0493	-0.0313	0.2966	0.0288	0.0211	0.1995	-0.0176	0.2734	-4.7407	14.0051	29.0702
15	1.3991	0.7025	1.1603	1.8861	1.3686	1.3896	0.0592	0.1484	0.0076	0.3126	0.0633	-0.1516	0.1291	0.1083	-0.1225	0.3307	0.0172	-0.0124	0.1803	-0.0148	0.2576	1.8064	13.9251	36.5591
16	1.0174	0.225	0.0917	0.952	-0.6475	0.5025	0.0211	0.01	0.1305	-0.0539	0.0088	0.0832	0.0474	-0.0032	-0.0299	0.3329	0.0246	0.0042	0.1683	-0.0128	0.2808	-8.2081	10.7241	31.1511
17	0.9803	-0.6542	-0.6009	1.4051	-2.1665	7.6923	0.1258	-0.0473	-0.0704	-0.1358	0.1416	0.1981	0.3244	-0.0629	-0.2673	0.2958	0.0119	-0.0112	0.1487	0.0078	0.2685	-8.3787	-9.1713	31.1639
18	1.9342	2.4343	-0.029	4.9548	0.9644	0.5317	0.121	-0.4222	0.1792	0.6335	-0.0874	0.1504	0.2301	0.2476	-0.0336	0.4402	0.004	-0.1402	0.2228	-0.0373	0.1336	3.7991	9.1715	46.1257
19	1.6128	0.0812	-2.1571	7.3344	1.179	3.1116	0.1527	-0.0331	0.0542	0.0765	-0.0316	-0.2659	-0.1929	0.0459	-0.1212	0.2162	-0.027	-0.0452	0.1843	-0.0445	0.252	13.8308	19.9764	37.1122
20	0.9313	-0.2018	-0.5225	3.3501	0.4786	0.3414	-0.2839	-0.103	-0.0578	0.386	0.2778	-0.0059	0.2059	0.1125	0.0061	0.3625	0.0233	-0.1439	0.1545	-0.0004	0.2018	4.6308	-0.3108	40.9698
21	2.8129	3.7645	-3.7064	5.1528	-5.1491	5.1975	-0.2903	-0.1089	-0.0951	-0.4158	-0.0033	-0.2449	0.4271	-0.1248	0.2936	0.2808	0.0143	0.1423	0.3465	-0.0277	0.2376	-29.1121	10.1078	30.1193
22	3.8903	-0.7568	-0.8489	1.1813	-0.0324	0.2357	0.0094	-0.2373	0.0022	0.1539	0.0162	0.1446	-0.0419	-0.0133	-0.0256	0.2439	0.0668	0.0877	0.407	-0.0114	0.1608	-23.5217	23.3966	36.7993
23	1.217	1.7409	-2.7937	7.0028	-0.1482	9.6947	0.2745	-0.3872	-0.0539	0.4826	-0.5172	0.066	-0.5558	0.9272	0.2427	0.2603	-0.0666	0.0119	0.2407	0.0907	0.2895	-14.1309	37.2338	32.3346
24	0.9236	-0.2532	-0.8455	0.0766	0.2232	0.8038	0.1486	0.1326	0.1665	-0.0439	0.001	-0.0742	-0.0793	-0.2105	-0.1496	0.2707	-0.0358	0.0412	0.3509	0.0405	0.2618	-23.3658	16.5084	24.7315
25	2.4258	4.3492	-0.4517	7.8024	-0.7968	0.1251	-0.1475	0.0536	0.0397	-0.3081	0.0654	0.0941	-0.006	-0.139	0.0821	0.2303	0.2375	0.0242	0.5431	-0.1296	0.2322	-32.6015	25.9623	17.766
26	2.748	-1.207	-0.6183	0.6654	0.0106	0.6661	-0.1085	0.4581	0.1807	0.1517	-0.0289	-0.1406	-0.2178	-0.3909	0.1374	0.5632	0.1656	-0.0893	0.3086	0.0147	0.1431	-20.8323	31.4256	7.9949
27	12.1006	10.6596	1.8042	11.5102	-0.4646	2.2784	-0.2122	0.0889	0.0337	-0.1261	0.0573	-0.1779	-0.0741	0.0009	0.1548	0.2651	0.0193	-0.0064	0.1254	0.0102	0.2862	-13.8481	43.0343	16.0865
28	11.7132	-9.4914	0.1564	7.6962	-0.152	0.1383	0.4808	0.1758	-0.0075	-0.3724	-0.1989	0.042	-0.1833	0.0783	-0.2819	0.7195	-0.2743	0.009	0.1169	-0.0008	0.6945	-6.8477	43.653	12.581
29	0.1814	-0.7433	-0.3888	5.2752	3.2597	2.0848	-0.1926	-0.0747	-0.0253	-0.3255	0.2158	-0.0104	-0.4093	0.0682	-0.0233	0.7533	0.0639	0.0525	0.2067	0.0029	0.135	-9.2918	27.7782	8.7366
30	0.9975	0.9058	0.7339	6.2953	-0.2796	0.7202	-0.1439	0.4093	-0.1778	0.0051	0.2387	-0.4316	-0.1629	0.2801	-0.0948	0.3421	-0.0363	0.0969	0.3412	0.0107	0.148	-7.8208	21.0145	3.0499
31	1.2696	-1.8425	-0.2689	7.6606	-0.0562	2.2808	0.1564	0.2203	-0.0741	0.081	-0.0213	-0.1937	0.0219	-0.141	-0.1352	0.216	-0.0004	0.0046	0.2117	-0.0106	0.2493	-7.9411	9.4395	12.1812
32	2.4342	4.1823	-2.8919	7.2247	-4.9959	3.5405	0.0735	0.0405	0.0638	0.1795	0.1104	0.1987	-0.1964	0.108	-0.1839	0.2859	-0.0842	0.1217	0.4185	-0.0276	0.2654	-3.5258	29.7039	16.4202
33	1.4187	1.6728	1.0701	3.5522	3.3493	3.593	0.3163	0.1468	-0.1352	-0.1134	-0.139	-0.2657	-0.355	-0.3096	-0.1772	0.3328	0.0652	0.07	0.1686	0.0605	0.2051	-13.0268	15.623	16.5134
34	0.4446	-0.1495	-0.2	0.8693	0.5155	1.5458	0.0778	0.1087	0.052	-0.0656	0.086	-0.133	-0.1286	-0.2414	-0.1638	0.2699	0.0612	0.0341	0.2673	0.0395	0.2211	-19.7223	19.0506	19.7384
35	0.4187	-0.523	-0.3977	1.1386	1.0417	1.2983	0.138	0.0749	0.0862	0.0479	0.0212	-0.1027	0.0361	-0.24	-0.1592	0.2443	0.1035	0.074	0.3417	0.0595	0.2285	-21.5263	18.4442	18.8511
36	3.5221	4.5357	1.8071	7.2032	0.1743	4.3348	0.0757	-0.6358	0.1043	0.1867	-0.6367	-0.1733	-0.092	-0.6318	0.561	0.1749	0.0497	0.1252	0.3373	-0.0701	0.2193	-34.3091	27.4449	33.073
37	2.9612	0.1262	-0.8257	2.5128	4.4697	8.3307	-0.5909	-0.0277	0.2687	0.0256	-0.2847	0.536	0.2788	-0.4616	0.8756	0.214	0.0822	-0.0107	0.4033	-0.045	0.1555	-35.5979	15.7256	14.5435
38	2.0398	-2.8735	2.9699	4.8813	-4.4064	4.3891	-0.1703	0.1969	0.0188	-0.2769	0.1131	-0.1428	-0.1397	0.1407	0.0572	0.5112	-0.0225	0.0661	0.518	-0.0416	0.0802	-23.4228	17.0091	-2.0282
39	0.8961	0.0195	0.0618	0.0073	0.0029	0.0108	-0.0236	0.2322	0.3383	-0.0162	-0.0142	0.0348	-0.0071	-0.0245	0.0378	0.1439	0.1327	-0.0898	0.3894	-0.0498	0.2503	-35.9975	21.0756	11.4778
40	10.2723	1.3366	0.6048	2.2874	2.9024	3.8736	0.3195	0.3027	0.3024	-0.0602	-0.3117	0.0842	-0.0709	-0.3622	-0.0078	0.2484	0.2154	0.0853	0.2581	-0.0018	0.2414	-30.4654	34.2175	24.8644
41	0.4915	0.0515	1.6173	1.1943	1.2217	7.0819	0.0562	0.001	-0.0013	-0.2058	0.2001	0.1206	-0.3255	0.0961	-0.2562	0.1949	0.0026	0.0741	0.3296	0.0559	0.2409	22.1452	35.9596	64.2949
42	4.4744	2.036	-5.3064	9.5089	3.6022	10.5131	0.1479	-0.1528	0.2869	-0.4747	0.2103	0.0886	-0.5316	0.3706	-0.3582	0.2366	-0.0637	0.0961	0.2605	-0.0316	0.2192	28.134	41.8983	75.8103
43	8.452	-5.0962	-3.0113	6.0399	7.2459	11.1829	-0.2237	-1.5296	-1.0477	0.0273	1.2536	-0.0022	-0.1552	1.424	-1.0299	0.0298	-0.0501	0.1154	0.6158	-0.1719	0.5404	31.4767	36.6833	87.2239
44	0.9855	0.1397	-0.492	0.1259	-0.2604	2.1553	0.1367	0.2221	0.0933	-0.0001	0.1273	-0.0649	-0.262	0.0108	-0.264	0.0997	-0.0032	0.0371	0.4482	-0.0149	0.2541	17.2063	32.952	70.2962
45	3.901	2.6998	-2.5099	5.6696	-1.3923	1.6517	-0.0353	-0.004	-0.2112	-0.2252	-0.0736	-0.1107	0.0164	0.0333	0.109	0.124	0.0492	-0.0657	0.3973	-0.0885	0.2164	22.8387	19.0131	67.4965
46	3.201	-0.8487	1.4884	0.8207	0.7164	2.775	0.2511	-0.0612	-0.0755	0.0567	-0.061	-0.079	0.3645	-0.2103	-0.1901	0.2019	-0.0064	-0.0952	0.3133	-0.0399	0.3225	13.6033	10.5465	78.163
47	0.0426	-0.1496	0.5141	1.0765	-1.2125	7.0666	0.0294	0.0246	0.0092	-0.0152	-0.0564	-0.2171	0.2496	0.2493	0.0269	0.1678	0.0666	-0.1127	0.2623	-0.0478	0.2921	23.0533	9.9342	81.6535
48	2.0778	0.9789	1.5478	7.4643	1.1437	2.2803	0.0778	0.1179	-0.1739	0.2891	0.0788	0.001	-0.0235	0.1573	-0.1565	0.2304	-0.015	-0.1225	0.2241	-0.009	0.2239	21.0164	9.668	93.9188
49	0.7034	-0.9524	-0.1968	1.4608	-0.2591	1.8425	-0.0504	-0.1049	-0.0029	0.1251	0.2649	0.0141	-0.1506	-0.2259	-0.2145	0.1552	-0.0399	-0.0568	0.3615	0.0091	0.283	8.0053	15.5522	84.0566
50	7.7932	-1.7458	3.063	2.2513	1.5393	3.8797	0.2538	-0.5177	-0.4946	-0.0328	0.1359	-0.0507	0.1337	-0.2454	-0.3897	0.173	-0.0701	-0.0803	0.3189	0.0911	0.2584	7.8883	6.7949	89.999
51	4.2819	-1.7108	3.4519	1.602	-1.8316	3.0199	0.1269	-0.1482	-0.3548	0.122	0.1673	0.1587	0.0216	-0.2507	-0.2942	0.0889	-0.0309	-0.0704	0.4533	0.0379	0.2712	-2.368	16.9463	77.1441
52	2.4745	1.075	-0.299	1.8029	1.9601	3.3112	0.1892	0.3647	-0.0655	0.0607	-0.0699	-0.0784	-0.0661	-0.3685	-0.1193	0.0225	0.0411	-0.0111	0.4643	0.0645	0.3243	-3.4096	28.4583	75.0526
53	4.9794	-0.6281	4.5734	5.6915	1.8875	5.283	-0.185	-0.3699	0.1504	0.0135	-0.0504	0.1874	-0.1787	-0.3949	0.2354	0.219	-0.0461	0.0027	0.3619	0.0575	0.1845	7.3965	23.3999	89.4401
54	5.0072	0.8717	1.696	4.8672	-3.6062	3.8033	-0.0491	-0.0506	0.1071	0.0526	-0.1145	-0.1167	-0.07	0.0755	0.1637	0.2093	0.0006	-0.0627	0.2655	0.0141	0.249	14.512	19.3849	91.0454
55	1.3317	0.7231	0.3375	0.4482	0.323	0.4539	-0.0724	0.0593	-0.072	-0.0377	0.051	-0.0341	-0.0408	-0.0007	0.0214	0.1181	0.0324	-0.0203	0.3881	0.0155	0.2635	9.7465	29.2282	74.4704
56	1.4343	0.6841	0.7892	0.5257	0.8611	1.7785	0.0292	0.201	0.0293	0.0654	0.0227	0.0286	0.0951	0.0889	-0.0518	0.1013	0.017	-0.0248	0.3998	-0.0076	0.2644	10.9821	25.2639	69.2181
57	2.3077	0.1714	-0.3609	1.1474	0.0621	0.757	0.0145	0.1589	0.1992	0.0347	0.0393	-0.1551	-0.0187	0.198	-0.0538	0.0036	0.0141	0.0093	0.464	-0.0121	0.2115	29.6023	30.8993	69.0558
58	8.5811	0.481	-2.2819	0.0317	-0.0785	1.4783	0.0686	-0.0124	0.1118	-0.0191	-0.0126	0.0128	-0.084	-0.1403	-0.056	0.2204	-0.0078	-0.0314	0.2595	-0.0459	0.2255	7.8304	12.8782	58.105
59	6.0524	1.8185	-0.704	0.6298	-0.625	2.367	-0.0391	0.4104	-0.4489	-0.0654	0.1304	-0.069	0.1339	-0.2125	-0.0913	0.1993	0.0031	-0.0952	0.2812	-0.1274	0.2686	9.6833	11.8436	63.4406
60	3.224	0.7468	0.49	0.5447	0.4298	0.3446	-0.2446	0.3565	-0.0573	0.2826	0.091	0.1897	0.2546	0.0849	0.1536	0.3385	0.0496	0.1637	0.4143	-0.0665	0.1819	30.4728	23.5607	66.5296
61	6.266	3.0784	-1.4332	1.5127	-0.7068	0.4332	-0.0505	-0.3162	-0.2134	-0.0166	-0.1563	-0.1059	-0.041	0.1455	0.2068	0.2348	0.0263	-0.0017	0.2531	0.0829	0.2923	19.0014	52.1588	71.9423
62	2.0653	2.4089	0.3561	3.4608	-0.1227	0.5765	-0.3122	0.2233	0.0585	-0.2123	0.2383	0.0092	-0.3284	0.0579	0.0739	0.4014	0.0443	0.0009	0.2549	0.0845	0.1298	2.4037	48.7806	69.6209
63	3.9651	0.2165	5.2246	0.6729	-1.9989	14.8683	-0.5698	0.1001	-0.0464	-0.3396	0.2245	-0.1246	0.3751	-0.8025	0.3453	0.2978	-0.2211	0.1396	0.4201	0.016	0.2484	-13.1907	38.5114	71.7328
64	0.2366	-0.0294	0.3925	0.9295	-0.6875	1.1004	-0.1902	0.1821	-0.0356	0.0061	0.2556	0.075	-0.338	0.0984	-0.0654	0.3074	-0.0258	0.0241	0.346	0.0263	0.2553	7.4035	47.883	79.6834
65	4.4374	2.9747	-1.4583	4.1354	-5.2216	8.9011	-0.6597	-0.3103	0.2322	0.059	0.0563	-0.1648	-0.7475	-0.3903	0.6035	0.3276	0.2361	0.0131	0.3113	0.0196	0.2391	-2.2187	56.9107	86.968
66	4.1808	1.8084	-1.1704	4.8873	-1.3085	0.4856	-0.1475	0.2052	-0.0091	0.456	0.1285	-0.0143	-0.0589	-0.0842	0.019	0.181	0.105	0.0847	0.494	-0.0497	0.1159	-4.3756	43.7425	97.0329
67	7.2191	-1.4282	-3.954	3.3854	2.2194	2.8349	0.5559	-0.0848	0.1602	0.1087	-0.3917	-0.1387	-0.2183	-0.1404	-0.1642	0.1811	0.0895	0.1031	0.3855	-0.0403	0.213	-11.5946	47.673	96.3814
68	2.6963	2.6553	2.6493	7.1985	-1.9203	7.0791	-0.2622	-0.1362	0.0931	-0.2344	0.2002	0.116	-0.2805	-0.4583	0.0619	0.1133	0.0515	0.0486	0.3286	-0.0405	0.239	-14.0535	41.6193	89.3846
69	6.0052	-1.4763	-9.0452	10.7003	2.1982	13.7551	0.0796	-0.0125	-0.2018	0.2495	-0.2273	0.5565	0.0284	0.0026	0.1478	0.198	-0.0717	-0.1091	0.1837	-0.0916	0.3757	-20.2016	34.0343	86.4228
70	0.1605	-0.437	-0.3329	1.1938	0.9101	0.6996	-0.0708	0.0139	-0.0782	0.1778	-0.0451	0.2148	0.115	-0.0242	0.1159	0.1517	-0.0683	0.1755	0.331	-0.085	0.4522	-19.3775	31.4605	93.5753
71	5.2105	-2.0078	1.8567	0.9803	-0.8154	0.7214	0.3988	-0.0837	-0.241	-0.0442	-0.3016	0.1258	0.0549	0.0971	-0.0973	0.1957	-0.075	0.0045	0.6499	-0.0436	0.099	-3.5884	33.427	95.5641
72	14.7347	-4.8321	-2.8956	3.4028	4.337	6.9248	0.1779	-0.0596	-1.048	0.1359	-0.3295	0.3332	0.2706	-0.5444	0.1515	0.1587	-0.0964	0.097	0.3234	0.0114	0.2244	-9.7728	27.8968	99.4504
73	7.2024	1.2675	-1.0649	1.3173	-1.6008	1.9858	-0.3502	-0.2981	-0.129	0.2161	0.1256	-0.1799	-0.2869	-0.2188	0.2246	0.3565	-0.0827	0.0952	0.4309	-0.0124	0.1051	-0.887	31.2756	103.0044
74	2.9744	-0.3312	0.9309	0.6755	1.0955	2.608	0.3799	-0.0094	-0.3449	-0.0164	-0.0161	-0.1247	0.0469	-0.0936	-0.3638	0.3031	0.0044	-0.0801	0.2694	0.0338	0.2546	16.1025	34.1933	97.0956
75	2.4759	4.5127	1.7098	8.3178	3.1185	1.1809	0.2275	-0.167	-0.1239	0.3758	-0.1418	-0.2758	0.151	-0.1133	-0.0856	0.2013	-0.02	0.0334	0.3519	0.0278	0.2367	-0.8187	26.9078	88.5978
76	1.5644	1.4813	-1.5938	1.4091	-1.5164	1.6548	-0.0603	0.1469	0.0391	-0.0535	0.1891	0.0394	0.0415	-0.2297	-0.1288	0.1131	0.0242	0.0685	0.4124	0.119	0.3368	-1.2807	32.8352	87.4347
77	0.8653	-0.4292	1.0338	0.5452	-0.051	2.2052	0.0188	-0.0176	-0.1062	-0.0104	0.1434	0.0691	-0.288	-0.0151	-0.1622	0.2841	0.0869	0.0636	0.326	0.0453	0.1971	8.5214	44.2372	87.4215
78	2.7911	1.4583	2.9862	3.8198	1.884	3.4558	-0.5488	0.0746	-0.0346	0.0037	0.3945	0.1684	-0.6289	-0.0811	0.1542	0.2362	0.1308	0.0178	0.3835	0.0258	0.2691	-4.3941	54.4999	72.2854
79	2.3141	-0.1147	1.6937	1.5222	-2.0502	5.9842	-0.163	-0.4187	0.2563	0.2133	-0.0221	0.0654	-0.7129	-0.0609	0.1851	0.2918	0.1429	0.003	0.2202	-0.0674	0.1444	5.3886	56.1384	96.298
80	4.8869	8.04	-1.0964	15.7022	0.575	2.5462	-0.2746	0.1415	0.2722	-0.4353	0.2453	0.5281	0.0487	-0.0738	0.0293	0.1633	0.1005	-0.0047	0.2631	0.0457	0.2511	-11.689	51.4714	78.6968

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	23 - 37
2	X-RAY DIFFRACTION	2	A	38 - 44
3	X-RAY DIFFRACTION	3	A	45 - 53
4	X-RAY DIFFRACTION	4	A	54 - 73
5	X-RAY DIFFRACTION	5	A	74 - 92
6	X-RAY DIFFRACTION	6	A	93 - 111
7	X-RAY DIFFRACTION	7	A	112 - 122
8	X-RAY DIFFRACTION	8	A	123 - 149
9	X-RAY DIFFRACTION	9	A	150 - 160
10	X-RAY DIFFRACTION	10	A	161 - 173
11	X-RAY DIFFRACTION	11	A	174 - 179
12	X-RAY DIFFRACTION	12	A	180 - 185
13	X-RAY DIFFRACTION	13	A	186 - 192
14	X-RAY DIFFRACTION	14	A	193 - 221
15	X-RAY DIFFRACTION	15	A	222 - 244
16	X-RAY DIFFRACTION	16	A	245 - 255
17	X-RAY DIFFRACTION	17	A	256 - 272
18	X-RAY DIFFRACTION	18	A	273 - 285
19	X-RAY DIFFRACTION	19	A	286 - 292
20	X-RAY DIFFRACTION	20	A	293 - 311
21	X-RAY DIFFRACTION	21	B	24 - 32
22	X-RAY DIFFRACTION	22	B	33 - 46
23	X-RAY DIFFRACTION	23	B	47 - 53
24	X-RAY DIFFRACTION	24	B	54 - 73
25	X-RAY DIFFRACTION	25	B	74 - 83
26	X-RAY DIFFRACTION	26	B	84 - 109
27	X-RAY DIFFRACTION	27	B	110 - 119
28	X-RAY DIFFRACTION	28	B	120 - 128
29	X-RAY DIFFRACTION	29	B	129 - 143
30	X-RAY DIFFRACTION	30	B	144 - 172
31	X-RAY DIFFRACTION	31	B	173 - 180
32	X-RAY DIFFRACTION	32	B	181 - 192
33	X-RAY DIFFRACTION	33	B	193 - 204
34	X-RAY DIFFRACTION	34	B	205 - 231
35	X-RAY DIFFRACTION	35	B	232 - 262
36	X-RAY DIFFRACTION	36	B	263 - 272
37	X-RAY DIFFRACTION	37	B	273 - 282
38	X-RAY DIFFRACTION	38	B	283 - 292
39	X-RAY DIFFRACTION	39	B	293 - 304
40	X-RAY DIFFRACTION	40	B	305 - 312
41	X-RAY DIFFRACTION	41	C	24 - 37
42	X-RAY DIFFRACTION	42	C	38 - 43
43	X-RAY DIFFRACTION	43	C	44 - 53
44	X-RAY DIFFRACTION	44	C	54 - 73
45	X-RAY DIFFRACTION	45	C	74 - 87
46	X-RAY DIFFRACTION	46	C	88 - 99
47	X-RAY DIFFRACTION	47	C	100 - 116
48	X-RAY DIFFRACTION	48	C	117 - 130
49	X-RAY DIFFRACTION	49	C	131 - 143
50	X-RAY DIFFRACTION	50	C	144 - 152
51	X-RAY DIFFRACTION	51	C	153 - 171
52	X-RAY DIFFRACTION	52	C	172 - 179
53	X-RAY DIFFRACTION	53	C	180 - 185
54	X-RAY DIFFRACTION	54	C	186 - 194
55	X-RAY DIFFRACTION	55	C	195 - 221
56	X-RAY DIFFRACTION	56	C	222 - 254
57	X-RAY DIFFRACTION	57	C	255 - 279
58	X-RAY DIFFRACTION	58	C	280 - 285
59	X-RAY DIFFRACTION	59	C	286 - 299
60	X-RAY DIFFRACTION	60	C	300 - 312
61	X-RAY DIFFRACTION	61	D	23 - 28
62	X-RAY DIFFRACTION	62	D	29 - 46
63	X-RAY DIFFRACTION	63	D	47 - 53
64	X-RAY DIFFRACTION	64	D	54 - 74
65	X-RAY DIFFRACTION	65	D	75 - 83
66	X-RAY DIFFRACTION	66	D	84 - 98
67	X-RAY DIFFRACTION	67	D	99 - 108
68	X-RAY DIFFRACTION	68	D	109 - 114
69	X-RAY DIFFRACTION	69	D	115 - 122
70	X-RAY DIFFRACTION	70	D	123 - 128
71	X-RAY DIFFRACTION	71	D	129 - 143
72	X-RAY DIFFRACTION	72	D	144 - 149
73	X-RAY DIFFRACTION	73	D	150 - 162
74	X-RAY DIFFRACTION	74	D	163 - 179
75	X-RAY DIFFRACTION	75	D	180 - 185
76	X-RAY DIFFRACTION	76	D	186 - 201
77	X-RAY DIFFRACTION	77	D	202 - 255
78	X-RAY DIFFRACTION	78	D	256 - 274
79	X-RAY DIFFRACTION	79	D	275 - 306
80	X-RAY DIFFRACTION	80	D	307 - 312

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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

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Protein , 4 types, 4 molecules ACBD

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-Download

-Validation report

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-Assembly

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-Protein , 4 types, 4 molecules ACBD

-Non-polymers , 4 types, 486 molecules

-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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 4 types, 4 molecules ACBD

-
Non-polymers , 4 types, 486 molecules

-
Experimental details

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Experiment

-
Sample preparation

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Data collection

-
Processing

+
About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi