PDB-3ic8: The Crystal Structure of a GST-like protein from Pseudomonas syri...

ID or keywords:

Entry

Database: PDB / ID: 3ic8

Title

The Crystal Structure of a GST-like protein from Pseudomonas syringae to 2.4A

Components

uncharacterized GST-like proteinprotein

Keywords

structural genomics / unknown function / Glutathione / transferase / pseudomonas / syringae / PSI / MCSG / Midwest Center for Structural Genomics / Protein Structure Initiative

Function / homology

Function and homology information

Glutaredoxin - #110 / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily ...
Similarity search - Domain/homology

Biological species

Pseudomonas syringae pv. tomato (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.4 Å

Authors

Stein, A.J. / Chhor, G. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The Crystal Structure of a GST-like protein from Pseudomonas syringae to 2.4A
Authors: Stein, A.J. / Chhor, G. / Freeman, L. / Joachimiak, A.

History

Deposition	Jul 17, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 1, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3ic8.cif.gz	220.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3ic8.ent.gz	190.4 KB	Display	PDB format
PDBx/mmJSON format	3ic8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3ic8_validation.pdf.gz	456.4 KB	Display	wwPDB validaton report
Full document	3ic8_full_validation.pdf.gz	489.5 KB	Display
Data in XML	3ic8_validation.xml.gz	42.4 KB	Display
Data in CIF	3ic8_validation.cif.gz	59.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ic/3ic8 ftp://data.pdbj.org/pub/pdb/validation_reports/ic/3ic8	HTTPS FTP

-
Related structure data

Similar structure data	5vye-d 1svv-1 6k8t-d 7dst-d 6wwf-d 4i2z-d 7e9l-d 7luf-1 5mfe-d 4x4u-3 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 - HomologyF&H Search
Other databases	TargetDB: APC61706

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (6) #255 - Mar 2021 Cisplatin and DNA similarity (5)

Deposited unit

A: uncharacterized GST-like proteinprotein

B: uncharacterized GST-like proteinprotein

C: uncharacterized GST-like proteinprotein

D: uncharacterized GST-like proteinprotein

137 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

A: uncharacterized GST-like proteinprotein

B: uncharacterized GST-like proteinprotein

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

3

C: uncharacterized GST-like proteinprotein

D: uncharacterized GST-like proteinprotein

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

Unit cell

Length a, b, c (Å)	84.671, 102.266, 148.336
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

authors state that biological unit is the same as asymmetric unit.

#1: Protein	uncharacterized GST-like proteinprotein Mass: 34357.977 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria) Strain: pv. tomato / Gene: PSPTO1263 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q887M8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

uncharacterized GST-like proteinprotein

Mass: 34357.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas syringae pv. tomato (bacteria)
Strain: pv. tomato / Gene: PSPTO1263 / Plasmid: pMCSG19 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q887M8

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.34 Å³/Da / Density % sol: 47.36 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 3350, 0.2M Succinic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2009
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.25→50 Å / Num. obs: 61123 / % possible obs: 99.7 % / Redundancy: 4.9 % / R_merge(I) obs: 0.092 / Net I/σ(I): 12.3
Reflection shell	Resolution: 2.25→2.33 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.662 / % possible all: 100

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	refmac_5.5.0054	refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-3000		phasing
SHELX		phasing
MLPHARE		phasing
DM		phasing
ARP/wARP		model building
Coot		model building

Refinement

Resolution: 2.4→48.34 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.934 / SU B: 19.962 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.376 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.246	2560	5.1 %	RANDOM
R_work	0.192	-	-	-
obs	0.195	50340	98.5 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 25.53 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.01 Å²	0 Å²	0 Å²
2-	-	0.06 Å²	0 Å²
3-	-	-	-0.07 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→48.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8401	0	0	178	8579

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	8629
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.269	1.949	11758
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.441	5	1087
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.889	23.003	363
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.004	15	1274
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.797	15	53
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	1317
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	6625
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	0.423	1.5	5475
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.786	2	8771
X-RAY DIFFRACTION	r_scbond_it	1.309	3	3154
X-RAY DIFFRACTION	r_scangle_it	2.086	4.5	2987
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.4→2.46 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.312	177	-
R_work	0.256	3514	-
obs	-	-	99.76 %

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	3.7483	-0.1444	0.4717	1.4364	-0.488	1.369	-0.0368	-0.0538	-0.1066	-0.1482	0.069	0.0296	0.0446	-0.0022	-0.0322	0.1992	-0.0026	0.0081	0.1458	-0.0104	0.1865	-29.7464	5.3654	-18.3102
2	2.477	-1.473	2.1322	1.9837	-1.5467	1.9128	0.1173	-0.0207	-0.1506	-0.1695	-0.038	-0.0126	0.1413	0.0167	-0.0793	0.2254	0.0076	0.0297	0.128	0.013	0.1861	-29.3168	3.3672	-23.8
3	8.0048	3.5151	-1.8397	1.8309	-1.3008	1.3838	0.1747	-0.2878	0.0821	0.1328	-0.0495	0.0384	0.0474	-0.0637	-0.1253	0.3687	0.0719	-0.0433	0.3731	0.0112	0.3137	-20.9822	5.1735	-6.5971
4	5.7555	-0.529	3.5961	6.8234	1.658	3.6031	0.0879	-0.23	0.6069	0.4626	-0.1263	-0.2311	-0.2529	-0.0248	0.0385	0.3766	-0.0325	0.0904	0.3388	-0.0269	0.3028	-21.3146	10.9957	-13.0126
5	2.6648	-2.3302	0.8894	3.0354	-0.89	1.6304	-0.0437	-0.2903	0.1162	0.0152	-0.0053	0.0925	0.1098	0.0411	0.049	0.24	-0.0057	0.0307	0.1687	0.0003	0.2622	-21.1356	11.3136	-24.8016
6	2.0281	-1.2157	0.2489	2.4081	-0.0215	1.2544	-0.0186	0.0466	-0.0337	-0.2782	0.055	-0.1705	0.2183	0.2356	-0.0364	0.2097	-0.0209	0.0195	0.1004	0.0094	0.1701	-30.3408	19.2902	-32.7432
7	5.9533	3.1224	-2.8414	6.2503	-2.4883	4.4429	0.0551	-0.0562	-0.3526	0.3171	-0.3154	-0.1442	-0.2646	0.2304	0.2603	0.2251	0.0077	-0.0293	0.0979	0.0098	0.1558	-40.5599	21.5768	-14.712
8	4.0978	2.7232	-5.7407	4.2555	-2.3848	8.8874	0.1842	0.2949	0.2959	0.15	-0.0413	0.6733	-0.2907	-0.5839	-0.1429	0.3587	0.031	0.0521	0.4005	0.0089	0.2962	-48.332	15.6952	-4.8503
9	1.7342	-2.8137	1.4309	8.6115	1.9878	5.7724	-0.2048	-0.0742	0.1593	0.464	0.038	-0.2228	-0.0398	-0.1695	0.1668	0.2542	-0.028	0.0289	0.2017	0.0128	0.2579	-47.5705	27.9535	-12.1025
10	0.09	0.431	0.0695	6.0451	2.9898	9.0757	0.0538	-0.0175	-0.0579	-0.0545	0.0122	0.3783	-0.0755	-0.3087	-0.0661	0.1251	-0.021	-0.019	0.1048	0.0212	0.2415	-49.1989	25.2729	-26.9149
11	2.1442	0.108	-1.3029	1.1945	-1.4016	3.3863	-0.0612	-0.052	0.0341	-0.1321	0.0171	0.0661	0.1302	-0.099	0.0441	0.198	-0.022	-0.0112	0.1106	-0.0154	0.1737	-43.4177	15.5855	-24.7472
12	0.2457	1.242	0.17	6.6177	0.8844	0.1216	0.0916	-0.0365	0.1325	0.2642	-0.1639	0.3845	0.0685	-0.0329	0.0723	0.358	-0.0716	0.011	0.3068	0.0307	0.3816	-52.9969	17.8434	-23.2113
13	5.5476	-0.1155	0.2924	0.9891	0.832	0.7548	-0.0433	-0.0929	-0.6984	-0.1171	-0.0393	0.248	-0.0409	-0.0246	0.0826	0.3847	-0.0098	-0.0363	0.1576	0.0062	0.3339	-39.8073	6.2358	-27.5029
14	3.0874	0.4865	-0.0744	3.6413	-1.0579	1.5706	-0.0893	-0.0606	-0.1834	-0.3314	-0.0533	-0.5447	0.1824	0.2041	0.1426	0.2477	0.0634	0.0351	0.1964	-0.038	0.2832	-12.3976	4.1333	-22.6975
15	2.5637	0.2319	1.2765	4.4459	-2.105	1.7743	-0.3196	-0.1071	0.4555	0.2208	-0.0146	-0.3791	-0.2674	-0.0242	0.3342	0.2823	-0.0328	-0.0593	0.271	-0.0516	0.5422	-10.0165	25.8597	-19.9405
16	10.3046	-6.9134	-9.6758	4.6476	6.5009	9.0968	-0.2436	0.0993	-0.2495	0.2515	-0.036	0.1796	0.3178	-0.1149	0.2796	0.6555	0.099	-0.0124	0.7647	0.0005	0.4937	-18.9094	18.8331	-7.9151
17	3.1058	0.6139	-2.8505	1.2984	0.0886	2.9775	-0.0355	-0.1216	-0.0159	-0.0125	0.1717	-0.2729	0.0234	0.2217	-0.1363	0.1656	0.0275	0.0243	0.2409	0.0071	0.3876	-10.5507	20.6421	-23.4044
18	1.7092	-3.435	3.1105	8.5268	-5.0392	7.4701	0.1235	0.0063	-0.0185	-0.0851	-0.0827	-0.0644	0.2549	0.4562	-0.0408	0.2036	0.0126	-0.0071	0.3216	-0.0317	0.3627	-9.502	13.2992	-18.1767
19	2.068	0.6507	-0.6794	0.3602	0.0368	0.8405	-0.0798	0.0682	-0.0714	0.1017	-0.0127	-0.0932	0.0957	0.0379	0.0926	0.3322	-0.0481	-0.0567	0.227	0.0076	0.388	-13.2111	12.4902	-18.1501
20	1.0034	-1.9813	0.3447	3.9559	-0.6676	0.1265	-0.3995	-0.3401	0.0294	0.7831	0.475	-0.1231	-0.1376	-0.161	-0.0755	0.5461	-0.0109	-0.0568	0.8314	0.0481	0.6583	-13.7796	24.4398	-12.6638
21	3.6254	0.4957	0.889	3.0947	0.1551	2.131	-0.1462	0.175	-0.2578	-0.1063	-0.0136	-0.0857	0.1914	0.0623	0.1597	0.2258	0.0058	0.038	0.1462	0.0207	0.1213	-55.213	-1.6266	-16.7396
22	3.3892	-0.4613	2.3636	2.0585	0.0365	1.9579	0.0471	0.3368	-0.155	-0.0859	-0.0174	-0.2286	0.2487	0.2898	-0.0297	0.2763	0.0184	0.0607	0.1859	-0.0231	0.2032	-52.5791	-8.8209	-17.629
23	6.5331	-0.389	-3.2707	1.828	0.036	3.3327	-0.0048	-0.1145	0.6591	0.1298	-0.1263	0.0696	-0.2097	0.2083	0.1311	0.301	0.0201	-0.0455	0.2369	0.0021	0.2757	-64.4303	7.125	-18.2958
24	5.4474	1.0957	-1.0069	1.6659	-0.7808	3.3122	0.0588	-0.1644	0.1753	0.2049	-0.1537	-0.3331	-0.0839	-0.2774	0.0949	0.2383	-0.0164	0.0153	0.1659	-0.0186	0.1704	-64.87	-2.4514	-13.7581
25	0.5253	1.2179	1.3532	7.0655	2.2781	3.6894	0.0412	0.0144	0.0149	0.0778	0.0323	0.1616	0.1045	0.0279	-0.0735	0.2471	-0.0304	0.048	0.1718	0.0094	0.2423	-60.2873	-9.1705	-8.1664
26	5.5356	1.4554	0.3488	3.6148	1.9693	7.5337	0.0343	0.0254	-0.2546	-0.0995	0.1581	0.1187	0.3676	-0.1182	-0.1923	0.3165	0.0118	0.0327	0.1113	0.003	0.2789	-55.0928	-17.8475	-8.9084
27	4.7253	-0.7954	0.9824	2.0485	-2.7806	3.7789	0.1055	-0.05	-0.3951	-0.3949	-0.0283	0.0706	0.5547	0.0293	-0.0772	0.3123	0.0115	0.0344	0.1567	0.0462	0.2428	-52.7451	-13.216	4.0559
28	0.7153	2.259	-1.5746	8.2572	-2.5639	8.9062	0.0491	0.0261	0.0325	0.0981	0.0067	0.1294	0.0274	-0.1555	-0.0558	0.2124	0.0579	-0.0132	0.1693	-0.0182	0.1784	-47.8675	4.2421	1.4788
29	9.3991	6.9215	-1.8291	10.0082	-1.5713	0.3685	-0.0894	-0.1394	0.1833	0.3074	0.1238	-0.3472	-0.0204	0.0078	-0.0344	0.3582	-0.0393	0.0003	0.3218	-0.0127	0.28	-41.0202	15.7364	-3.5227
30	1.4534	-1.7039	0.4391	8.9309	1.4027	6.2883	0.0898	-0.3235	0.2134	0.0658	-0.0514	0.016	-0.3098	0.1102	-0.0383	0.1477	-0.0399	0.0222	0.2412	0.0065	0.1848	-42.2989	6.501	8.4464
31	2.0125	0.8112	1.0936	1.5076	1.0409	3.192	0.0394	-0.0226	-0.3107	-0.0487	-0.0138	-0.1743	0.4902	0.5803	-0.0256	0.2915	0.0964	0.0313	0.2473	0.041	0.2304	-39.9184	-12.2872	2.4479
32	2.138	2.6199	-1.354	5.2056	-1.4469	1.7932	-0.1586	-0.1656	-0.0685	-0.1717	0.0157	-0.2173	0.0979	0.1914	0.1428	0.1818	0.033	0.0091	0.1804	0.0063	0.1504	-41.6757	1.0993	-5.194
33	0.6187	-0.5328	1.0147	2.2387	1.1855	4.3824	-0.0014	-0.0708	0.143	-0.1068	0.0893	-0.5607	-0.1286	0.2342	-0.0879	0.2221	0.0289	0.0137	0.3714	0.0821	0.3191	-34.6273	-3.1449	-1.0198
34	9.0156	1.8143	1.7916	2.4998	-0.4193	7.4733	-0.0805	0.435	-0.3307	-0.1325	0.2432	-0.1671	0.1778	1.2613	-0.1627	0.2665	0.0734	0.0393	0.3255	-0.0329	0.2357	-40.0375	-9.6738	-9.8291
35	10.428	-3.7823	7.577	1.569	-2.8026	5.5247	-0.159	0.1937	0.1667	0.0259	0.0001	-0.1102	-0.1268	0.1085	0.1589	0.2722	-0.0024	0.0134	0.2591	-0.0096	0.2433	-51.7644	-5.6744	-23.2858
36	7.9909	4.0604	-3.2525	6.3173	-3.6304	2.3449	-0.2075	0.3829	0.1391	-0.4817	0.1899	0.2411	0.2608	-0.2496	0.0175	0.2501	-0.046	-0.023	0.3649	-0.0624	0.2524	-68.6964	-3.3519	-26.2621
37	1.2381	-0.1638	1.0432	0.2709	-0.672	4.6527	0.0545	-0.1241	-0.3607	0.0501	0.0411	0.0617	0.4577	-0.4893	-0.0956	0.2719	-0.0464	0.0596	0.305	0.0037	0.2716	-75.7234	-9.7706	-2.9521
38	2.5433	-2.4316	2.2745	5.5908	-1.1006	6.2592	0.0065	0.0371	0.0311	0.0706	-0.2348	0.013	0.0337	-0.3924	0.2283	0.1806	-0.0781	0.0528	0.2525	-0.0245	0.2349	-74.1495	-6.2309	-4.8475
39	2.989	-2.3971	4.5158	3.0396	-3.6122	9.0416	0.0341	0.0457	-0.037	-0.0122	-0.0809	0.0857	0.2137	-0.2126	0.0467	0.2264	-0.0144	0.0304	0.2782	-0.0182	0.2898	-75.0969	-5.0564	-11.1255
40	2.112	0.0693	-0.1135	0.9629	0.4976	1.5597	-0.0921	-0.0523	0.0266	0.0438	0.0227	0.1854	-0.3099	-0.4896	0.0694	0.254	0.0191	0.03	0.2854	0.001	0.1932	-72.6122	-2.2523	-7.6614
41	4.085	-0.2293	-1.2498	2.0932	-0.2136	1.3604	0.0594	0.1177	-0.3663	-0.0254	0.0269	-0.0362	0.0013	-0.0078	-0.0863	0.2265	-0.026	-0.024	0.14	-0.0026	0.2134	-44.9667	1.0054	-47.3015
42	1.7375	1.7719	-1.4498	3.1749	0.188	3.7893	-0.0424	0.2046	0.0671	-0.2816	0.1354	0.1317	-0.0587	-0.1478	-0.093	0.2075	0.0026	-0.0148	0.1765	-0.0047	0.2135	-42.6424	2.3402	-44.3163
43	2.8202	1.7534	-0.6577	7.4718	-4.8963	4.4065	-0.2618	0.3265	-0.0176	-0.6178	0.3612	0.8745	0.0385	-0.2932	-0.0995	0.4377	0.003	-0.0844	0.4585	-0.0058	0.4355	-38.4934	4.5931	-59.5555
44	1.8028	2.6882	-1.1055	4.3499	-0.7179	3.6427	-0.1649	0.147	-0.0175	-0.2834	0.1426	0.0551	0.0106	-0.039	0.0222	0.2134	0.0028	-0.0161	0.2538	-0.0255	0.2867	-35.9298	-5.3679	-48.4015
45	5.7112	4.8736	0.3628	5.1911	1.2511	5.5872	0.1385	-0.0855	0.0825	0.233	-0.1562	-0.3435	-0.1129	0.3734	0.0178	0.2137	0.0369	-0.0483	0.1412	0.0197	0.2461	-37.598	-14.5812	-36.7397
46	0.3416	-1.1692	-0.1975	4.7802	0.2175	0.3951	0.004	-0.022	0.0325	0.1149	0.0015	-0.1158	-0.0615	0.1011	-0.0055	0.1842	0.0265	0.0177	0.1818	0.02	0.1778	-45.8564	-20.9057	-45.8024
47	0.8309	-0.823	-0.0641	8.1577	1.4063	0.3829	0.0193	0.304	0.3991	-0.6339	-0.0358	0.1932	-0.268	-0.0103	0.0164	0.3008	-0.0011	-0.0017	0.2958	0.0945	0.3443	-58.923	-11.7604	-54.1489
48	1.7124	0.777	-0.6085	4.4556	-0.1335	0.2215	-0.0904	0.2615	0.0691	-0.215	0.0967	0.5209	0.0194	-0.0918	-0.0063	0.1884	-0.0167	-0.0194	0.1262	0.0088	0.2514	-63.7561	-20.1859	-49.2739
49	4.7034	2.7495	0.3564	6.577	3.4164	8.3602	0.1602	-0.3147	0.0369	0.4871	-0.2618	0.1944	0.2239	-0.3836	0.1016	0.2341	0.0039	0.0222	0.1604	0.0297	0.2158	-57.8587	-21.7334	-33.0133
50	7.6633	3.8141	3.6519	5.0829	-0.7098	3.7462	0.0403	-0.3605	-0.0743	0.214	-0.001	-0.0483	-0.1232	-0.3258	-0.0392	0.2195	0.0255	0.0285	0.0745	-0.0394	0.204	-47.3149	-17.2874	-36.4577
51	6.4347	-1.4188	1.6926	7.4445	-1.946	1.7208	-0.0902	0.2571	0.1939	0.0799	0.1009	0.1884	-0.1158	0.0557	-0.0106	0.1934	-0.0143	0.0134	0.1008	-0.0112	0.2159	-55.3622	-8.9409	-43.789
52	1.1788	1.5013	1.5178	2.5404	0.6866	4.5392	0.0276	-0.1224	0.3347	-0.0072	0.0881	0.6411	0.1388	-0.5044	-0.1157	0.2128	0.0211	0.0485	0.3294	-0.0018	0.475	-65.6023	-10.0006	-41.7608
53	3.22	0.2719	-1.5925	0.0595	0.2644	5.1678	0.0466	-0.7603	0.0107	0.01	-0.1797	0.024	-0.0233	-0.5496	0.1331	0.3583	-0.0254	0.0397	0.3801	-0.0774	0.3168	-54.7028	-9.9953	-34.4887
54	0.84	0.4899	-0.486	4.4334	-1.6683	5.596	0.1573	-0.1787	0.1452	0.2713	-0.0439	0.2298	-0.4707	0.2231	-0.1134	0.185	-0.0405	-0.0563	0.1092	0.0113	0.2266	-40.5714	6.5432	-43.1187
55	2.7735	-0.4103	0.3221	5.13	1.7734	1.6369	0.0384	-0.0413	0.025	-0.0406	0.0929	-0.9254	-0.0056	0.2098	-0.1314	0.2209	-0.0723	0.0214	0.3635	0.0552	0.2809	-24.0056	-5.759	-51.2013
56	3.6041	2.2727	-1.0607	8.0892	-1.2146	0.3742	-0.2113	0.5584	-0.0329	-0.8233	0.2629	-0.1516	0.0782	-0.1406	-0.0516	0.3935	-0.0033	0.0385	0.3828	-0.0388	0.295	-30.4539	-13.7166	-64.5545
57	5.3422	0.5742	0.9125	5.8926	-0.7278	2.4077	0.0682	0.4327	-0.1171	-0.3305	-0.1668	-0.2935	0.0089	0.5078	0.0986	0.1835	0.0146	0.0681	0.2474	-0.018	0.2057	-28.7301	-10.7177	-59.3445
58	0.8981	-0.3683	1.0242	8.9738	-1.6499	1.804	0.0178	0.1597	0.175	-0.174	0.027	-0.1453	-0.2192	0.2437	-0.0448	0.2774	0.0004	0.0358	0.2972	-0.0123	0.2814	-27.5014	-2.2797	-59.3374
59	1.7981	0.4026	0.1121	0.8479	1.0685	1.5253	0.0316	0.1441	0.1548	-0.2154	0.1259	0.0053	-0.2707	0.2711	-0.1575	0.2711	-0.0185	0.0036	0.3106	-0.0152	0.3018	-31.0814	-4.3308	-56.5539
60	8.0733	-3.5146	0.2689	3.2005	-0.103	0.0172	-0.0839	0.9711	0.0084	-0.6986	0.0556	-0.0276	0.022	0.0229	0.0284	0.5384	-0.158	0.0198	0.4624	-0.0364	0.3278	-34.5545	-11.9332	-66.471
61	6.729	-0.1481	0.0612	0.1431	-0.015	0.0515	-0.0477	-0.5297	-0.3681	0.0754	0.0162	0.1415	-0.1502	-0.0839	0.0315	0.507	0.1042	-0.0121	0.4862	-0.0689	0.266	-74.2934	6.263	-42.0433
62	1.4431	1.447	-2.9124	1.5194	-2.8942	5.9067	0.1672	-0.0686	0.0474	0.0548	-0.0594	-0.0894	-0.4307	0.0534	-0.1078	0.4976	0.1536	0.0135	0.4527	-0.1306	0.4278	-78.0557	13.7972	-46.7624
63	1.1796	0.037	0.0945	2.5493	-2.2281	2.1835	0.0071	-0.866	0.1846	0.0896	0.1973	-0.0659	-0.1714	-0.3072	-0.2044	0.524	0.1117	-0.023	0.6833	-0.1299	0.4071	-77.7502	6.7793	-37.241
64	3.8222	-5.1568	0.8183	8.3228	-2.7829	2.2455	-0.2642	-0.2997	0.2843	0.4625	0.1875	-0.4171	-0.2327	0.1822	0.0766	0.3796	-0.013	-0.0116	0.6168	0.0347	0.3342	-78.8365	-6.9868	-37.2057
65	9.0148	-3.7585	-1.3853	5.3996	3.139	1.9283	-0.0681	-0.1925	-0.3499	0.1014	0.1386	-0.0253	0.0383	0.1001	-0.0705	0.3712	0.025	-0.0146	0.4595	0.017	0.3141	-77.5481	-1.7428	-44.936
66	1.5363	2.135	-1.7419	3.3666	-3.5449	5.17	-0.0164	-0.1497	0.0866	0.1564	-0.029	0.0731	-0.481	-0.2084	0.0454	0.3007	0.0876	0.017	0.5368	-0.023	0.2845	-86.3989	3.9929	-47.3576
67	4.5332	-2.6681	4.908	1.9606	-2.7927	5.3405	-0.2243	-0.4168	-0.0585	0.2428	0.1732	0.4348	-0.2589	-0.4978	0.0511	0.417	0.0974	0.0863	0.3735	-0.0959	0.413	-88.1271	14.8662	-53.8206
68	8.0115	-1.2088	1.847	4.7758	-0.9299	2.3312	-0.1219	-0.3084	-0.1965	0.0697	0.1936	-0.0257	-0.3441	-0.1523	-0.0716	0.2468	0.0544	0.0025	0.2517	-0.0774	0.1715	-78.3824	8.8414	-63.2315
69	9.2719	-2.7483	6.5158	3.1667	-2.4415	4.6905	0.0914	-0.2926	-0.1575	0.036	-0.0227	-0.1538	0.0345	-0.1846	-0.0687	0.2832	0.02	0.0036	0.2384	-0.0281	0.2295	-61.9752	3.8276	-56.9382
70	0.2354	-0.4702	-0.1626	2.54	-2.9384	6.7984	-0.123	-0.01	0.0175	0.0652	-0.1181	-0.1313	0.5525	0.3093	0.241	0.3207	0.0044	-0.0045	0.3351	-0.0066	0.3482	-54.2385	1.563	-62.2711
71	1.5276	-1.8604	-1.7821	4.8859	1.3706	3.3797	-0.111	-0.1115	0.1212	-0.1555	0.0582	-0.1869	-0.3767	0.3949	0.0528	0.3751	-0.0958	-0.0749	0.2146	-0.0376	0.2903	-61.5513	11.0319	-66.3708
72	6.9041	-3.2423	-2.3225	7.0671	-1.8951	8.2022	0.1605	-0.0876	1.0078	0.0989	0.1892	0.0776	-0.3152	0.1258	-0.3497	0.3926	0.0067	-0.0545	0.246	-0.0771	0.3497	-71.3527	23.1468	-64.5826
73	6.3562	-1.0828	4.1776	1.9234	-3.3335	6.7	-0.1936	-0.2659	0.1327	0.2671	0.1877	0.0379	-0.489	-0.3701	0.0059	0.4271	0.079	-0.029	0.2901	-0.1705	0.2409	-72.946	14.0216	-55.7797
74	2.0785	1.7561	-2.2201	1.9742	-1.2685	3.1372	0.3098	-0.1613	0.142	0.0114	-0.3881	0.3043	-0.741	-0.1005	0.0784	0.5355	-0.0343	-0.1122	0.3353	-0.0956	0.3836	-57.5287	14.0579	-53.1566
75	6.1111	-2.6547	-4.1249	6.3982	3.6233	3.4619	0.3185	-0.1675	0.1661	-0.2922	-0.2064	-0.0505	-0.3953	0.0361	-0.112	0.4509	-0.0247	-0.0225	0.3659	-0.0321	0.3947	-62.068	21.831	-60.1734
76	2.3449	2.0162	-0.9336	2.5248	-0.9201	3.8856	0.2096	-0.6838	0.1315	0.517	-0.2156	0.1411	-0.4574	-0.1489	0.006	0.3453	0.1893	0.0381	0.499	-0.0891	0.2428	-83.311	8.2221	-41.1412
77	3.9684	1.0514	-2.8104	0.3212	-0.5829	2.6427	0.0457	-0.2721	-0.1603	0.0793	-0.1969	-0.0042	0.3006	-0.3526	0.1512	0.3612	-0.1258	-0.0186	0.5935	0.0388	0.4685	-92.2529	-10.7526	-57.0889
78	2.1589	-0.0893	1.1211	3.791	-2.396	6.3677	0.1182	-0.2554	0.0134	0.1983	0.0337	-0.1306	0.2328	-0.2758	-0.1519	0.2058	-0.0079	0.0216	0.4798	0.028	0.2436	-88.0526	-7.3781	-52.6221
79	0.6561	-2.2581	0.5515	7.9002	-1.951	0.491	-0.0458	-0.1107	-0.0416	0.0077	0.1582	0.2268	0.0433	-0.0451	-0.1124	0.4172	-0.0369	-0.0107	0.6022	0.0498	0.385	-90.833	-9.7231	-42.3224
80	1.8055	1.1361	-2.4415	2.7068	-1.0324	5.921	0.0969	-0.3406	-0.1379	0.1761	0.2252	0.1164	0.2021	-0.3079	-0.322	0.2373	-0.0247	-0.0404	0.5974	0.1219	0.4058	-86.7871	-7.7162	-47.6665

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 18
2	X-RAY DIFFRACTION	2	A	19 - 35
3	X-RAY DIFFRACTION	3	A	36 - 45
4	X-RAY DIFFRACTION	4	A	46 - 55
5	X-RAY DIFFRACTION	5	A	56 - 74
6	X-RAY DIFFRACTION	6	A	75 - 98
7	X-RAY DIFFRACTION	7	A	99 - 110
8	X-RAY DIFFRACTION	8	A	111 - 116
9	X-RAY DIFFRACTION	9	A	148 - 156
10	X-RAY DIFFRACTION	10	A	157 - 168
11	X-RAY DIFFRACTION	11	A	169 - 200
12	X-RAY DIFFRACTION	12	A	201 - 209
13	X-RAY DIFFRACTION	13	A	210 - 225
14	X-RAY DIFFRACTION	14	A	226 - 246
15	X-RAY DIFFRACTION	15	A	247 - 265
16	X-RAY DIFFRACTION	16	A	266 - 272
17	X-RAY DIFFRACTION	17	A	273 - 282
18	X-RAY DIFFRACTION	18	A	283 - 290
19	X-RAY DIFFRACTION	19	A	291 - 303
20	X-RAY DIFFRACTION	20	A	304 - 310
21	X-RAY DIFFRACTION	21	B	1 - 18
22	X-RAY DIFFRACTION	22	B	19 - 32
23	X-RAY DIFFRACTION	23	B	33 - 47
24	X-RAY DIFFRACTION	24	B	48 - 63
25	X-RAY DIFFRACTION	25	B	64 - 73
26	X-RAY DIFFRACTION	26	B	74 - 84
27	X-RAY DIFFRACTION	27	B	85 - 97
28	X-RAY DIFFRACTION	28	B	98 - 110
29	X-RAY DIFFRACTION	29	B	111 - 116
30	X-RAY DIFFRACTION	30	B	148 - 160
31	X-RAY DIFFRACTION	31	B	161 - 180
32	X-RAY DIFFRACTION	32	B	181 - 200
33	X-RAY DIFFRACTION	33	B	201 - 212
34	X-RAY DIFFRACTION	34	B	213 - 218
35	X-RAY DIFFRACTION	35	B	219 - 226
36	X-RAY DIFFRACTION	36	B	227 - 238
37	X-RAY DIFFRACTION	37	B	239 - 265
38	X-RAY DIFFRACTION	38	B	270 - 282
39	X-RAY DIFFRACTION	39	B	283 - 290
40	X-RAY DIFFRACTION	40	B	291 - 310
41	X-RAY DIFFRACTION	41	C	2 - 19
42	X-RAY DIFFRACTION	42	C	20 - 38
43	X-RAY DIFFRACTION	43	C	39 - 51
44	X-RAY DIFFRACTION	44	C	52 - 75
45	X-RAY DIFFRACTION	45	C	76 - 87
46	X-RAY DIFFRACTION	46	C	88 - 98
47	X-RAY DIFFRACTION	47	C	99 - 149
48	X-RAY DIFFRACTION	48	C	150 - 163
49	X-RAY DIFFRACTION	49	C	164 - 172
50	X-RAY DIFFRACTION	50	C	173 - 181
51	X-RAY DIFFRACTION	51	C	182 - 193
52	X-RAY DIFFRACTION	52	C	194 - 210
53	X-RAY DIFFRACTION	53	C	211 - 217
54	X-RAY DIFFRACTION	54	C	218 - 232
55	X-RAY DIFFRACTION	55	C	233 - 249
56	X-RAY DIFFRACTION	56	C	250 - 267
57	X-RAY DIFFRACTION	57	C	270 - 282
58	X-RAY DIFFRACTION	58	C	283 - 291
59	X-RAY DIFFRACTION	59	C	292 - 303
60	X-RAY DIFFRACTION	60	C	304 - 310
61	X-RAY DIFFRACTION	61	D	3 - 17
62	X-RAY DIFFRACTION	62	D	18 - 24
63	X-RAY DIFFRACTION	63	D	25 - 38
64	X-RAY DIFFRACTION	64	D	39 - 49
65	X-RAY DIFFRACTION	65	D	50 - 56
66	X-RAY DIFFRACTION	66	D	57 - 74
67	X-RAY DIFFRACTION	67	D	75 - 86
68	X-RAY DIFFRACTION	68	D	87 - 100
69	X-RAY DIFFRACTION	69	D	101 - 112
70	X-RAY DIFFRACTION	70	D	113 - 152
71	X-RAY DIFFRACTION	71	D	153 - 163
72	X-RAY DIFFRACTION	72	D	164 - 174
73	X-RAY DIFFRACTION	73	D	175 - 191
74	X-RAY DIFFRACTION	74	D	192 - 203
75	X-RAY DIFFRACTION	75	D	204 - 210
76	X-RAY DIFFRACTION	76	D	211 - 245
77	X-RAY DIFFRACTION	77	D	246 - 265
78	X-RAY DIFFRACTION	78	D	266 - 284
79	X-RAY DIFFRACTION	79	D	285 - 290
80	X-RAY DIFFRACTION	80	D	291 - 309

-
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