PDB-6vpu: 1.90 Angstrom Resolution Crystal Structure Phosphoadenosine Phosp...

ID or keywords:

Entry

Database: PDB / ID: 6vpu

Title

1.90 Angstrom Resolution Crystal Structure Phosphoadenosine Phosphosulfate Reductase (CysH) from Vibrio vulnificus

Components

Phosphoadenosine phosphosulfate reductase

Keywords

OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / CysH

Function / homology

Function and homology information

phosphoadenylyl-sulfate reductase (thioredoxin) / phosphoadenylyl-sulfate reductase (thioredoxin) activity / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / hydrogen sulfide biosynthetic process / cytoplasm
Similarity search - Function

Biological species

Vibrio vulnificus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Minasov, G. / Shuvalova, L. / Dubrovska, I. / Wiersum, G. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 1.90 Angstrom Resolution Crystal Structure Phosphoadenosine Phosphosulfate Reductase (CysH) from Vibrio vulnificus
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Wiersum, G. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Feb 4, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 10, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	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

-
Download

PDBx/mmCIF format	6vpu.cif.gz	775.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6vpu.ent.gz	644.1 KB	Display	PDB format
PDBx/mmJSON format	6vpu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6vpu_validation.pdf.gz	311 KB	Display	wwPDB validaton report
Full document	6vpu_full_validation.pdf.gz	311.6 KB	Display
Data in XML	6vpu_validation.xml.gz	1.8 KB	Display
Data in CIF	6vpu_validation.cif.gz	29.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vp/6vpu ftp://data.pdbj.org/pub/pdb/validation_reports/vp/6vpu	HTTPS FTP

-
Related structure data

Related structure data	1surS S: Starting model for refinement
Similar structure data	4mqi-d 3sp9-1 5ytl-d 4u3y-3 2ofp-2 6vg3-2 2pmk-d 3gn6-1 1wr2-d 6dj6-1 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) 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) 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-IDP97132

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phosphoadenosine phosphosulfate reductase

B: Phosphoadenosine phosphosulfate reductase

C: Phosphoadenosine phosphosulfate reductase

D: Phosphoadenosine phosphosulfate reductase

E: Phosphoadenosine phosphosulfate reductase

F: Phosphoadenosine phosphosulfate reductase

G: Phosphoadenosine phosphosulfate reductase

H: Phosphoadenosine phosphosulfate reductase

hetero molecules

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

1

A: Phosphoadenosine phosphosulfate reductase

hetero molecules

defined by author
29.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phosphoadenosine phosphosulfate reductase

hetero molecules

defined by author
29.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Phosphoadenosine phosphosulfate reductase

defined by author
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Phosphoadenosine phosphosulfate reductase

hetero molecules

defined by author
30 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Phosphoadenosine phosphosulfate reductase

defined by author
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Phosphoadenosine phosphosulfate reductase

defined by author
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

G: Phosphoadenosine phosphosulfate reductase

defined by author
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

H: Phosphoadenosine phosphosulfate reductase

defined by author
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

9

A: Phosphoadenosine phosphosulfate reductase

F: Phosphoadenosine phosphosulfate reductase

hetero molecules

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

10

B: Phosphoadenosine phosphosulfate reductase

G: Phosphoadenosine phosphosulfate reductase

hetero molecules

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

11

C: Phosphoadenosine phosphosulfate reductase

H: Phosphoadenosine phosphosulfate reductase

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

12

D: Phosphoadenosine phosphosulfate reductase

E: Phosphoadenosine phosphosulfate reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	107.758, 76.637, 143.876
Angle α, β, γ (deg.)	90.000, 102.890, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Phosphoadenosine phosphosulfate reductase / 3'-phosphoadenylylsulfate reductase / PAPS reductase / thioredoxin dependent / PAPS ...3'-phosphoadenylylsulfate reductase / PAPS reductase / thioredoxin dependent / PAPS sulfotransferase / PAdoPS reductase Mass: 29752.385 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (strain CMCP6) (bacteria) Strain: CMCP6 / Gene: cysH, VV1_1404 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q8CWK6, phosphoadenylyl-sulfate reductase (thioredoxin)
#2: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2009 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.45 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein: 9.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, Screen: PEG's II (D10), 0.2 M Sodium acetate, 0.1M Tris pH 8.5, 30% (w/v) PEG 4000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2019 / Details: C(111)
Radiation	Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.9→30 Å / Num. obs: 180003 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / B_iso Wilson estimate: 23.2 Å² / R_merge(I) obs: 0.08 / R_pim(I) all: 0.039 / R_rim(I) all: 0.09 / R_sym value: 0.08 / Χ²: 1.009 / Net I/σ(I): 19.5
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 5 % / R_merge(I) obs: 0.744 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8938 / CC_1/2: 0.768 / CC star: 0.932 / R_pim(I) all: 0.362 / R_rim(I) all: 0.83 / R_sym value: 0.744 / Χ²: 1.007 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1sur

1sur

Resolution: 1.9→29.8 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.946 / SU B: 5.718 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.126
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2064	9062	5 %	RANDOM
R_work	0.1724	-	-	-
obs	0.1741	170880	99.89 %	-

Solvent computation

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

Displacement parameters

B_iso max: 132.31 Å² / B_iso mean: 28.212 Å² / B_iso min: 11.52 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.4 Å²	0 Å²	0.67 Å²
2-	-	0.14 Å²	0 Å²
3-	-	-	-0.04 Å²

Refinement step

Cycle: final / Resolution: 1.9→29.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14612	0	39	2104	16755
B_iso mean	-	-	64.58	34.5	-
Num. residues	-	-	-	-	1801

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	15227
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	13938
X-RAY DIFFRACTION	r_angle_refined_deg	1.275	1.632	20653
X-RAY DIFFRACTION	r_angle_other_deg	0.352	1.572	32436
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.389	5	1842
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.116	23.534	829
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.055	15	2707
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.531	15	76
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	1888
X-RAY DIFFRACTION	r_gen_planes_refined	0.054	0.02	16993
X-RAY DIFFRACTION	r_gen_planes_other	0.049	0.02	3167

LS refinement shell

Resolution: 1.9→1.949 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.261	659	-
R_work	0.246	12438	-
all	-	13097	-
obs	-	-	99.14 %

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	7.5629	-2.0131	-0.7322	4.507	0.3006	1.4924	-0.1474	-0.5629	0.4073	0.4735	0.1854	-0.0941	-0.1602	0.172	-0.038	0.0816	-0.0215	-0.0192	0.1184	0.0066	0.0481	-27.428	22.291	41.827
2	0.8161	0.0034	-0.0241	0.5749	0.0293	0.3933	0.0183	-0.013	-0.0624	0.0289	-0.0252	-0.0302	0.0414	0.128	0.0069	0.0928	0.0021	0.0038	0.1126	0.0258	0.0577	-40.868	0.889	35.969
3	4.1153	0.1854	4.9622	0.0222	0.3487	8.4665	-0.1158	-0.0378	0.2372	0.0014	-0.018	-0.0058	-0.1803	-0.0132	0.1338	0.0601	-0.0171	-0.0072	0.0385	0.0079	0.0538	-49.655	9.87	36.67
4	1.165	0.181	-0.3616	3.1785	0.7917	2.0375	0.0158	0.0594	0.0274	-0.2545	-0.0391	-0.1079	-0.1055	0.1282	0.0233	0.0372	0.0024	-0.008	0.1428	0.0415	0.0331	-29.273	7.423	31.441
5	4.7618	0.5096	-0.9112	2.5664	0.6294	2.8181	0.0566	0.3922	0.106	-0.2531	0.0254	-0.2255	0.0212	0.0993	-0.082	0.099	0.0014	0.0273	0.0812	0.0021	0.0269	-41.068	-4.707	21.716
6	3.0645	0.9064	-5.0598	13.9929	6.3658	13.6043	0.0498	0.0545	0.0299	0.4366	-0.2886	0.5422	0.0952	-0.3288	0.2389	0.0465	-0.0021	0.0038	0.1231	0.0098	0.0422	-44.869	-2.773	13.109
7	7.0325	-1.3864	-1.2879	2.4999	1.297	2.4123	0.4933	0.4759	1.3119	-0.4378	0.0955	-0.1208	-0.8771	-0.5404	-0.5888	0.3523	0.1951	0.2221	0.2957	0.1564	0.4404	-49.541	22.327	62.476
8	1.682	-0.4454	0.3751	0.7379	-0.2457	0.8333	-0.0385	-0.0692	0.0148	0.0235	0.0249	0.0091	0.0288	-0.1104	0.0136	0.0655	0.0047	0.0206	0.092	-0.0191	0.0468	-36.485	2.515	69.257
9	11.1997	-3.1359	3.884	13.4183	-3.3315	5.195	-0.0511	-0.7596	0.4655	0.7177	-0.2502	-0.0623	-0.6999	-0.1422	0.3013	0.1944	-0.0142	0.0188	0.0881	-0.0433	0.0789	-53.274	14.568	79.057
10	1.4848	-0.5192	0.1062	0.8085	-0.5325	1.5846	-0.1423	-0.2286	-0.1409	0.1212	0.1796	0.1197	0.0441	-0.3164	-0.0373	0.0574	-0.0269	0.0499	0.1668	-0.0187	0.051	-46.663	0.56	75.427
11	2.6013	2.4614	-4.0677	4.5492	-1.446	8.9924	-0.006	-0.0892	0.0988	-0.0813	0.1708	0.0398	-0.006	0.3405	-0.1649	0.1254	-0.021	0.0603	0.197	-0.0697	0.0509	-39.14	-1.745	87.688
12	9.2408	4.1644	-5.3521	2.0174	-2.8699	4.5977	0.7445	-0.8967	0.3118	0.3473	-0.3419	0.2034	-0.4491	0.3312	-0.4026	0.1613	-0.0423	0.0264	0.1839	-0.03	0.1836	-35.623	10.692	76.324
13	3.7936	-0.1776	-2.3287	2.0949	0.2688	3.2978	0.342	0.0724	0.3375	-0.2685	-0.0092	0.1102	-0.3579	-0.1671	-0.3328	0.0782	0.0363	0.0201	0.063	0.0033	0.0501	-35.112	20.13	-8.157
14	1.9799	-0.1633	0.266	0.78	0.0761	0.7246	0.0078	-0.1331	-0.0401	0.0256	-0.0186	0.0228	0.061	0.0073	0.0108	0.0817	0.0209	-0.0003	0.131	0.0097	0.0677	-18.735	0.926	-0.681
15	2.4362	-0.348	0.0968	0.2185	0.0351	0.7575	-0.0083	-0.138	0.2045	0.1322	0.0009	-0.0701	-0.0573	0.0666	0.0075	0.1176	-0.0091	-0.0359	0.0873	-0.03	0.0625	-15.262	12.501	2.667
16	15.1794	-5.1548	23.7975	24.2433	1.9657	41.7967	-0.686	-0.603	0.3641	0.3366	0.372	-0.706	-1.0364	-0.8736	0.314	0.2776	0.0301	-0.035	0.2548	0.0269	0.214	-31.492	19.227	10.017
17	1.166	-0.2942	-0.2193	0.7309	-0.7425	1.89	0.0254	-0.164	-0.0103	0.0933	0.0339	0.0854	-0.0708	-0.0336	-0.0592	0.0678	-0.011	0.0012	0.1393	-0.0226	0.0653	-33.214	7.302	3.223
18	10.4672	4.3806	-1.3029	3.2485	-0.7831	1.6728	0.1045	-0.6033	0.2204	0.1654	-0.0948	0.1374	-0.1195	-0.0558	-0.0096	0.0645	0.0122	0.0048	0.1298	-0.0103	0.0065	-20.642	-0.071	14.438
19	5.4368	0.5914	-2.0181	3.7592	-0.6731	1.5849	-0.0582	0.2739	0.3872	-0.3881	0.0917	0.0867	-0.2073	-0.1988	-0.0335	0.1829	0.0075	0.0116	0.1584	0.0082	0.1765	-94.983	63.152	28.673
20	1.4137	-0.235	0.0703	0.8116	-0.169	0.4852	-0.0119	-0.0991	-0.045	-0.0512	0.0377	0.0594	0.0908	-0.0785	-0.0258	0.0796	-0.0268	0.0133	0.1016	-0.0119	0.0469	-84.646	39.962	32.177
21	2.3883	-0.8655	0.5218	0.527	-0.5938	1.404	-0.0864	-0.0927	0.3282	0.0025	0.0373	-0.0995	-0.0429	0.021	0.0491	0.0706	-0.0194	0.0059	0.05	-0.0446	0.0762	-79.645	48.574	34.473
22	5.0191	-2.173	-0.3004	9.5072	-6.7959	5.8895	0.1749	-0.5792	0.0093	0.677	-0.1095	0.2963	-0.4848	0.2857	-0.0654	0.2627	-0.0145	0.0565	0.1418	-0.0665	0.1542	-98.348	52.962	45.51
23	1.3021	-0.2474	0.3422	0.9144	-0.6308	1.2813	-0.0303	-0.2407	-0.0311	0.0317	0.1425	0.1922	0.0582	-0.1515	-0.1122	0.0713	-0.0345	0.0392	0.1469	-0.0044	0.0584	-93.004	40.088	39.392
24	4.2882	1.6078	-1.7727	0.7986	-1.8176	8.1219	0.254	-0.0671	0.5699	0.0856	0.0209	0.2236	-0.0738	0.1992	-0.2749	0.1027	-0.0183	0.0475	0.2402	-0.0113	0.0879	-86.213	41.218	46.788
25	8.1997	-4.4371	0.3516	4.3947	-0.5355	0.1322	0.1405	0.5084	-0.1392	-0.2142	-0.07	0.0837	0.0145	-0.0084	-0.0705	0.0578	0.0416	-0.0179	0.1163	-0.0511	0.0898	-54.643	29.491	-2.098
26	1.3011	0.0287	-0.695	0.4904	0.1756	1.3181	0.0052	-0.101	0.0335	0.0106	0.0022	-0.0557	-0.0038	0.2133	-0.0074	0.0382	0.0248	-0.0049	0.0778	0.0057	0.0904	-53.913	37.011	21.459
27	1.4334	-0.013	0.0515	1.1103	-0.9466	0.9719	-0.0223	0.1338	-0.0575	0.0185	0.0596	0.0806	0.0951	-0.0167	-0.0373	0.0834	0.026	0.0092	0.0337	-0.0077	0.0498	-60.753	29.665	18.388
28	5.8962	0.4669	-1.4005	7.8111	-3.7873	2.0714	0.0782	-0.477	-0.3878	-0.436	0.0909	0.5159	0.1962	0.055	-0.1691	0.2315	0.0781	-0.0672	0.0817	0.0268	0.1385	-43.351	21.293	17.133
29	1.0825	-0.0481	-0.7657	0.8626	-0.1038	2.145	-0.006	-0.1241	-0.0704	0.0526	0.0069	-0.1604	0.1062	0.4651	-0.0009	0.017	0.0396	-0.0242	0.1463	0.0026	0.1186	-44.672	32.561	22.665
30	4.3125	-7.6743	-0.0817	15.2632	1.5188	4.9836	0.0472	-0.0097	-0.2028	-0.0534	0.1037	0.1586	0.1583	-0.0302	-0.1509	0.0504	-0.034	-0.0505	0.0595	0.011	0.0929	-44.249	17.585	34.745
31	12.6083	0.6679	0.8009	0.4834	-1.1425	3.2017	0.1937	-0.5262	0.3108	0.0487	-0.0315	0.0669	-0.0729	-0.0701	-0.1622	0.1347	-0.1528	0.0449	0.2193	0.0252	0.2018	-71.995	-12.785	70.871
32	1.4919	-0.0162	-0.41	1.1581	0.0933	1.5919	0.0909	-0.1679	0.0378	0.1152	-0.0889	0.1478	-0.0135	-0.1863	-0.002	0.054	-0.0529	0.0134	0.0924	-0.0079	0.0933	-69.475	-2.423	46.961
33	1.832	0.2236	-0.128	1.1847	1.5601	2.1705	-0.0962	-0.3191	-0.223	0.2167	0.0317	0.038	0.3514	0.131	0.0646	0.2295	-0.0315	0.0143	0.1382	0.0431	0.1598	-63.947	-10.293	50.176
34	2.6272	-1.1943	-2.236	8.5275	2.2565	2.1069	-0.2485	-0.1585	-0.4163	-0.1648	-0.0226	0.0221	0.2002	0.1522	0.2711	0.2958	0.0361	-0.1461	0.1682	-0.0979	0.3837	-80.634	-18.181	52.532
35	0.7877	0.6619	-0.1966	0.8236	0.1027	2.7404	0.1555	-0.1166	-0.03	0.0557	-0.1035	0.2415	0.0563	-0.4958	-0.052	0.1779	-0.0878	-0.0051	0.312	0.0122	0.3869	-79.755	-6.712	46.051
36	1.2573	2.6782	0.5228	6.9857	2.3368	1.3893	0.2404	-0.3617	-0.1564	0.6087	-0.0516	-0.3999	0.1776	0.5607	-0.1888	0.537	-0.0236	-0.0975	0.6069	-0.0617	0.5803	-72.195	-15.952	46.942
37	9.8685	-0.7584	-0.5839	0.2994	-0.0159	0.2415	0.0784	0.2258	0.1355	-0.172	0.0177	0.0884	-0.078	-0.0707	-0.0961	0.2007	0.066	-0.0267	0.2481	-0.0059	0.1853	-5.666	-10.007	35.305
38	1.4275	-0.3567	-0.6984	0.722	0.3442	1.3491	0.1601	0.1081	0.1382	-0.091	-0.0415	-0.1744	-0.2024	0.1252	-0.1187	0.0716	0.0299	0.0425	0.0896	0.0282	0.1412	-7.508	-0.526	58.966
39	1.5434	-0.1085	-0.0949	6.3319	-5.4639	4.8087	-0.0114	0.1063	-0.065	-0.3208	0.1228	0.0655	0.236	-0.1737	-0.1113	0.0915	0.04	0.0183	0.0707	0.019	0.081	-18.18	-13.153	60.922
40	2.8014	-0.6267	0.7064	1.8302	0.5646	4.7182	0.2984	0.1321	-0.2814	-0.1203	0.0172	-0.2145	0.1414	0.345	-0.3156	0.063	0.0578	0.0234	0.1114	0.0355	0.1579	1.305	-6.861	51.939
41	5.3234	2.1505	-1.581	3.6868	-1.0797	2.567	-0.0642	0.0215	-0.3934	0.116	0.0563	-0.4891	0.0045	0.3537	0.0079	0.0228	0.0301	-0.0207	0.1277	-0.0176	0.1747	0.88	-8.396	70.465
42	14.3479	-1.3919	-4.4213	14.8612	-5.6674	3.8865	-0.3103	0.4464	-0.5436	-0.1174	0.0202	-0.2441	0.1504	-0.1691	0.2901	0.1203	0.0645	0.0039	0.0826	-0.0127	0.0378	-7.371	-15.276	56.631
43	6.3195	5.3569	0.1241	9.5022	0.5758	0.155	0.1091	-0.3634	-0.0201	0.2095	-0.0836	0.2313	0.0282	0.0619	-0.0256	0.0293	-0.0248	-0.0233	0.1005	0.0318	0.0733	-5.69	27.045	35.001
44	1.0286	0.0094	-0.4981	0.3523	-0.3372	0.8341	0.0601	0.0388	-0.0336	-0.0536	0.0005	0.0413	-0.0288	-0.1616	-0.0606	0.0781	-0.0483	-0.0303	0.2123	-0.0171	0.1721	-8.568	36.821	13.469
45	2.4628	1.1808	1.1394	5.8829	4.698	6.3828	-0.0639	-0.0777	-0.1562	0.3818	0.1613	-0.0421	0.3726	0.1429	-0.0974	0.0583	-0.0204	0.0054	0.0776	0.0012	0.0331	3.004	27.9	10.031
46	7.9508	1.8517	0.3466	0.4364	0.095	1.9519	0.0131	0.0409	-0.6657	-0.0039	0.0351	-0.1645	0.2469	0.0111	-0.0482	0.0749	-0.0348	-0.0422	0.1037	-0.0332	0.1704	-10.513	31.853	18.777
47	8.351	0.9822	1.4088	1.9369	-2.7575	4.9337	0.1207	0.2007	-0.653	-0.2887	0.0055	-0.0725	0.5068	0.0649	-0.1261	0.073	-0.0241	-0.0415	0.1045	-0.0121	0.1381	-12.02	28.618	23.577
48	1.0321	0.6427	-0.8535	0.6446	-0.4105	1.3965	-0.007	0.2494	-0.0797	-0.076	0.0448	0.1349	0.0912	-0.5014	-0.0377	0.0705	-0.0539	-0.0778	0.3236	-0.0211	0.2224	-20.244	33.962	4.385

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 34
2	X-RAY DIFFRACTION	2	A	35 - 131
3	X-RAY DIFFRACTION	3	A	132 - 154
4	X-RAY DIFFRACTION	4	A	155 - 204
5	X-RAY DIFFRACTION	5	A	205 - 223
6	X-RAY DIFFRACTION	6	A	224 - 230
7	X-RAY DIFFRACTION	7	B	7 - 32
8	X-RAY DIFFRACTION	8	B	33 - 163
9	X-RAY DIFFRACTION	9	B	164 - 171
10	X-RAY DIFFRACTION	10	B	172 - 222
11	X-RAY DIFFRACTION	11	B	223 - 231
12	X-RAY DIFFRACTION	12	B	232 - 239
13	X-RAY DIFFRACTION	13	C	7 - 54
14	X-RAY DIFFRACTION	14	C	55 - 123
15	X-RAY DIFFRACTION	15	C	124 - 165
16	X-RAY DIFFRACTION	16	C	166 - 171
17	X-RAY DIFFRACTION	17	C	172 - 209
18	X-RAY DIFFRACTION	18	C	210 - 222
19	X-RAY DIFFRACTION	19	D	7 - 32
20	X-RAY DIFFRACTION	20	D	33 - 130
21	X-RAY DIFFRACTION	21	D	131 - 163
22	X-RAY DIFFRACTION	22	D	164 - 171
23	X-RAY DIFFRACTION	23	D	172 - 224
24	X-RAY DIFFRACTION	24	D	225 - 236
25	X-RAY DIFFRACTION	25	E	9 - 25
26	X-RAY DIFFRACTION	26	E	26 - 128
27	X-RAY DIFFRACTION	27	E	129 - 163
28	X-RAY DIFFRACTION	28	E	164 - 171
29	X-RAY DIFFRACTION	29	E	172 - 223
30	X-RAY DIFFRACTION	30	E	224 - 230
31	X-RAY DIFFRACTION	31	F	9 - 32
32	X-RAY DIFFRACTION	32	F	33 - 130
33	X-RAY DIFFRACTION	33	F	131 - 163
34	X-RAY DIFFRACTION	34	F	164 - 172
35	X-RAY DIFFRACTION	35	F	173 - 226
36	X-RAY DIFFRACTION	36	F	227 - 238
37	X-RAY DIFFRACTION	37	G	9 - 32
38	X-RAY DIFFRACTION	38	G	33 - 123
39	X-RAY DIFFRACTION	39	G	124 - 154
40	X-RAY DIFFRACTION	40	G	155 - 200
41	X-RAY DIFFRACTION	41	G	201 - 229
42	X-RAY DIFFRACTION	42	G	230 - 238
43	X-RAY DIFFRACTION	43	H	8 - 21
44	X-RAY DIFFRACTION	44	H	22 - 130
45	X-RAY DIFFRACTION	45	H	131 - 149
46	X-RAY DIFFRACTION	46	H	150 - 168
47	X-RAY DIFFRACTION	47	H	169 - 186
48	X-RAY DIFFRACTION	48	H	187 - 227

-
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

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi