PDB-4yqz: Crystal Structure of a putative oxidoreductase from Thermus Therm...

ID or keywords:

Entry

Database: PDB / ID: 4yqz

Title

Crystal Structure of a putative oxidoreductase from Thermus Thermophilus HB27 (TT_P0034, TARGET EFI-513932) in its APO form

Components

Putative oxidoreductase

Keywords

OXIDOREDUCTASE /

ENZYME FUNCTION INITIATIVE / EFI /

Structural Genomics

Function / homology

Function and homology information

oxidoreductase activity
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.807 Å

Authors

Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. ...

Citation

Journal: To be published
Title: Crystal Structure of a putative oxidoreductase from Thermus Thermophilus HB27 (TT_P0034, TARGET EFI-513932) in its APO form
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, ...

History

Deposition	Mar 13, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 25, 2015	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4yqz.cif.gz	363.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4yqz.ent.gz	310.2 KB	Display	PDB format
PDBx/mmJSON format	4yqz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yq/4yqz ftp://data.pdbj.org/pub/pdb/validation_reports/yq/4yqz	HTTPS FTP

-
Related structure data

Similar structure data	6q1v-d 2wdz-2 1dd7-1 6zns-d 2b3y-1 1o5o-d 1uls-2 7kr4-d 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: EFI-513932

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: Putative oxidoreductase

B: Putative oxidoreductase

C: Putative oxidoreductase

D: Putative oxidoreductase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	76.436, 65.752, 85.759
Angle α, β, γ (deg.)	90.000, 95.430, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Putative oxidoreductase / Mass: 27514.561 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_P0034 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q746L9
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 727 / 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: 1.95 Å³/Da / Density % sol: 37.08 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein, 10mM NAD; Reservoir (0.2 M Calcium chloride, 0.1M Tris: HCl, pH 8.50, 25%(w/v) PEG 4000); Cryoprotection (20% Diethylene glycol, 80% Reservoir)

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.9793 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 24, 2015 / Details: MIRRORS

Radiation

Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.8→100 Å / Num. obs: 76823 / % possible obs: 99.2 % / Redundancy: 7.5 % / B_iso Wilson estimate: 18.63 Å² / R_merge(I) obs: 0.066 / R_pim(I) all: 0.026 / R_rim(I) all: 0.069 / Χ²: 0.889 / Net I/av σ(I): 26.007 / Net I/σ(I): 9.8 / Num. measured all: 573677

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	Χ²	% possible all	R_rim(I) all
1.8-1.83	7.2	0.935	3794	0.802	0.37	0.822	98.8
1.83-1.86	7.2	0.844	3815	0.839	0.333	0.832	98.9	0.908
1.86-1.9	7.2	0.658	3806	0.885	0.26	0.842	99	0.708
1.9-1.94	7.3	0.524	3804	0.92	0.206	0.862	99	0.564
1.94-1.98	7.3	0.426	3831	0.945	0.167	0.852	99.1	0.458
1.98-2.03	7.4	0.341	3819	0.956	0.133	0.848	99.1	0.366
2.03-2.08	7.4	0.285	3812	0.968	0.111	0.859	99.2	0.306
2.08-2.13	7.5	0.239	3817	0.977	0.093	0.871	99.2	0.256
2.13-2.2	7.5	0.187	3841	0.983	0.073	0.858	99.4	0.2
2.2-2.27	7.5	0.16	3834	0.99	0.062	0.884	99.4	0.172
2.27-2.35	7.6	0.132	3831	0.99	0.051	0.876	99.6	0.141
2.35-2.44	7.6	0.117	3872	0.992	0.045	0.866	99.7	0.126
2.44-2.55	7.6	0.104	3821	0.993	0.04	0.869	99.7	0.112
2.55-2.69	7.6	0.093	3861	0.994	0.036	0.931	99.8	0.099
2.69-2.86	7.6	0.088	3877	0.994	0.034	1.074	99.8	0.094
2.86-3.08	7.6	0.08	3865	0.994	0.031	1.301	100	0.086
3.08-3.39	7.6	0.065	3892	0.996	0.025	1.245	100	0.07
3.39-3.88	7.6	0.046	3910	0.997	0.018	0.831	100	0.05
3.88-4.89	7.6	0.036	3898	0.998	0.014	0.623	100	0.039
4.89-100	7.4	0.037	3823	0.996	0.015	0.591	95.3	0.04

-
Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX	(phenix.refine: 1.9_1692)	refinement
PDB_EXTRACT	3.15	data extraction
HKL-3000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.807→25.091 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2095	3638	5.02 %
R_work	0.1643	68877	-
obs	0.1666	72515	93.3 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 194.05 Å² / B_iso mean: 26.8934 Å² / B_iso min: 7.17 Å²

Refinement step

Cycle: final / Resolution: 1.807→25.091 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6852	0	1	732	7585
B_iso mean	-	-	32.36	34.54	-
Num. residues	-	-	-	-	933

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6958
X-RAY DIFFRACTION	f_angle_d	1.078	9407
X-RAY DIFFRACTION	f_chiral_restr	0.043	1091
X-RAY DIFFRACTION	f_plane_restr	0.005	1234
X-RAY DIFFRACTION	f_dihedral_angle_d	13.554	2533

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8069-1.8307	0.2902	66	0.2132	1507	1573	52
1.8307-1.8557	0.2609	101	0.2115	1909	2010	68
1.8557-1.8822	0.2218	103	0.2053	2063	2166	73
1.8822-1.9103	0.2488	132	0.2031	2255	2387	80
1.9103-1.9402	0.2456	137	0.2074	2374	2511	84
1.9402-1.972	0.2474	132	0.2064	2532	2664	91
1.972-2.006	0.2618	143	0.1938	2744	2887	96
2.006-2.0424	0.2525	141	0.1924	2793	2934	99
2.0424-2.0817	0.2539	167	0.1869	2779	2946	99
2.0817-2.1241	0.2427	165	0.1797	2798	2963	99
2.1241-2.1703	0.218	144	0.1673	2792	2936	99
2.1703-2.2208	0.2301	141	0.1699	2809	2950	99
2.2208-2.2763	0.2144	137	0.1647	2840	2977	99
2.2763-2.3378	0.2022	153	0.1634	2790	2943	99
2.3378-2.4065	0.217	151	0.1595	2831	2982	99
2.4065-2.4841	0.2096	161	0.1711	2744	2905	99
2.4841-2.5728	0.2306	153	0.162	2807	2960	99
2.5728-2.6757	0.2128	140	0.1723	2810	2950	99
2.6757-2.7973	0.2178	161	0.1748	2803	2964	99
2.7973-2.9446	0.2053	140	0.171	2832	2972	99
2.9446-3.1288	0.1912	153	0.1641	2806	2959	99
3.1288-3.3698	0.1746	132	0.1604	2860	2992	100
3.3698-3.708	0.2263	152	0.1486	2835	2987	100
3.708-4.2423	0.1771	155	0.1327	2864	3019	100
4.2423-5.3364	0.1698	143	0.139	2881	3024	100
5.3364-25.0932	0.1959	135	0.1646	2819	2954	95

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	1.9084	-0.2638	-1.0832	2.2939	0.6053	3.9398	0.109	-0.2135	-0.023	0.3293	0.0124	0.3199	0.0516	-0.2247	-0.0186	0.1535	0.0179	0.0512	0.2234	0.003	0.2429	22.3616	39.5333	62.6219
2	1.5705	-1.4759	-0.1134	2.1198	1.7035	3.4945	0.0223	0.0103	-0.0539	0.1095	0.0053	0.3416	0.2524	-0.441	0.0523	0.0913	-0.0307	0.0069	0.1822	0.0253	0.2706	21.6039	33.1421	59.5483
3	0.8907	-0.19	-0.1223	1.2322	-1.2131	2.8217	0.134	0.0988	-0.1968	-0.1454	0.145	0.4895	0.2261	-0.4015	0.097	0.0881	-0.0034	0.0095	0.2577	0.0214	0.3558	18.1653	37.8101	53.2681
4	1.9078	0.4885	-0.6414	1.1127	-0.3318	1.3312	0.071	0.3084	0.224	-0.1707	-0.0848	0.3133	-0.1092	-0.145	0.0145	0.1514	0.0779	-0.0324	0.1907	0.0365	0.2372	26.7692	48.4446	47.6895
5	0.5157	0.393	0.1447	0.4439	-0.2097	0.6937	-0.0143	0.1179	-0.0509	-0.0078	-0.0264	0.154	-0.1191	-0.068	0.0285	0.0831	-0.0128	-0.0024	0.1331	-0.0162	0.1324	35.0269	38.2003	50.7367
6	2.4035	-1.0157	-1.8651	1.5705	0.5582	2.5882	-0.013	0.3475	0.0606	-0.1693	-0.0602	0.2909	-0.2847	-0.1969	0.0162	0.1115	0.0153	-0.0239	0.1911	0.0329	0.1491	41.7134	38.7975	42.2213
7	1.3009	-0.3531	0.5448	2.8448	1.138	2.9326	0.0899	-0.1087	0.4616	0.4021	-0.128	0.3061	-0.0168	0.0834	0.0099	0.1812	0.0226	0.0601	0.1317	-0.008	0.3298	33.9633	50.3982	56.9098
8	1.4713	-0.4114	-0.4575	0.279	-0.1009	0.8384	-0.0044	-0.1924	0.1048	0.0399	0.1565	-0.173	-0.0141	0.039	-0.0754	0.1459	-0.0083	0.0182	0.1347	-0.0184	0.1565	40.5935	33.119	56.6503
9	0.9316	-0.0727	-0.3534	1.6213	1.2655	2.4279	0.0293	0.08	0.1235	0.0349	-0.1699	0.2512	-0.1635	-0.1515	0.0071	0.0863	-0.0218	0.0223	0.1012	-0.0179	0.127	43.0937	41.5153	57.4525
10	0.8964	0.4988	0.3367	1.7049	1.1006	1.7527	0.0794	0.0923	0.0007	0.0279	-0.0508	0.0794	0.042	-0.2011	-0.0409	0.1252	-0.0077	0.0153	0.1324	-0.0126	0.1732	33.1956	29.5075	54.711
11	0.7609	0.2798	1.3308	0.8722	1.0409	3.6827	-0.1886	0.4914	-0.5608	-0.1468	0.0355	-0.1217	0.3965	0.184	-0.0194	0.3943	-0.0383	0.0215	0.2194	-0.0634	0.4228	33.8218	14.4179	54.017
12	0.7767	-0.0084	0.1633	1.176	0.0933	0.7137	0.0091	-0.1233	-0.0643	0.0606	0.031	0.064	0.055	-0.0573	-0.0575	0.1193	0.0091	0.0289	0.1393	0.0175	0.1415	34.5703	31.8229	66.1726
13	1.4045	0.6376	-0.0758	1.1293	-0.0832	1.2984	0.0458	0.187	0.1159	-0.0433	-0.0054	-0.1117	-0.089	0.1246	-0.0485	0.0863	-0.0168	0.0219	0.1862	0.0226	0.1134	70.7186	42.2199	40.9986
14	1.3134	0.2429	0.071	1.1078	-0.1894	0.7839	0.0128	0.143	0.1123	-0.038	0.0226	0.0027	-0.03	0.0188	-0.0422	0.0781	-0.0185	0.0061	0.1111	0.0064	0.0965	56	39.115	47.2731
15	1.4401	0.2224	0.2035	0.7012	-0.2571	1.3646	-0.0093	-0.0395	0.2687	0.1433	-0.0152	0.0672	-0.364	0.0718	-0.0097	0.1804	-0.0299	-0.0055	0.117	-0.0145	0.1362	65.8654	42.851	58.9243
16	1.7077	1.2662	-0.5283	3.589	-0.6834	1.9925	0.0071	-0.067	0.0981	-0.1556	0.2496	-0.2304	-0.0064	0.2491	-0.0617	0.146	-0.0334	-0.0741	0.2014	-0	0.2304	81.5474	29.6424	69.0713
17	3.2736	1.8497	0.1209	3.2306	-0.5359	1.313	-0.0246	0.109	-0.2713	-0.0588	-0.0058	-0.3274	0.206	0.3461	-0.0168	0.1193	0.0717	-0.1155	0.2354	-0.0045	0.1772	80.8065	23.2347	65.6162
18	0.5914	0.0668	-0.1052	0.856	-0.2094	0.9392	-0.0018	-0.2114	-0.3398	0.1508	-0.013	-0.3329	0.116	0.3857	0.0059	0.2002	0.0468	-0.1443	0.3142	0.0543	0.2919	80.8453	21.2706	78.7769
19	0.7224	0.0036	-0.1401	0.712	-0.1191	0.8931	-0.0245	-0.185	-0.1116	0.3236	0.0565	-0.1025	-0.0971	0.0643	-0.0193	0.2137	0.01	-0.0674	0.1279	0.0099	0.0955	65.0675	25.5806	76.6287
20	1.2975	-0.1382	0.0375	0.7039	-0.0473	1.49	-0.0011	-0.0759	-0.419	0.1553	-0.1379	-0.0049	0.559	0.0864	0.0025	0.2885	0.0181	0.0187	0.1254	0.0094	0.2183	66.9278	15.182	60.8637
21	0.9707	-0.071	-0.0246	1.2522	0.3178	1.1757	-0.053	-0.07	-0.0414	0.0969	-0.0033	-0.0073	0.0606	0.1297	0.0558	0.1036	-0.015	-0.0296	0.1179	0.0007	0.1013	68.602	30.2027	61.7606
22	1.9499	0.4008	0.9681	1.7929	0.1412	2.1203	-0.117	-0.211	-0.1364	0.1903	0.0592	0.6244	0.004	-0.209	0.012	0.2158	-0.009	0.1056	0.2547	0.0855	0.372	28.6074	22.226	81.7782
23	3.8928	1.0819	0.7554	0.9842	0.7035	1.8575	0.0001	-0.2213	0.0379	0.3029	-0.0633	0.4408	0.0407	-0.276	-0.0729	0.2141	0.016	0.2302	0.2302	0.0664	0.2946	29.5589	28.5243	84.9105
24	0.1708	-0.1048	0.1704	0.1255	-0.0912	0.1854	0.0218	-0.2938	-0.0399	0.458	0.107	0.3292	-0.0221	-0.1054	0.3045	0.5205	0.0887	0.2986	0.3388	0.2203	0.2716	35.7557	18.4093	91.6247
25	0.6644	-0.3327	-0.3766	0.3159	-0.1753	1.0255	-0.0199	-0.3374	-0.0178	0.3152	0.0779	0.1554	-0.0291	-0.1135	-0.0631	0.2833	0.0743	0.09	0.1673	0.0533	0.1464	45.4103	24.5253	84.862
26	3.276	1.2009	0.2564	0.8977	-0.026	0.5258	-0.0081	-0.393	-0.0313	0.4328	0.0042	-0.0313	-0.0361	0.0645	0.0127	0.3229	0.0341	0.0091	0.2325	0.0389	0.0896	55.6674	24.6356	88.5083
27	1.9573	1.1081	0.9927	2.4895	0.9761	2.3708	-0.1649	-0.0522	-0.1293	-0.0051	0.0563	0.3487	0.077	0.0151	0.0274	0.2611	-0.0001	0.0515	0.1587	0.0945	0.3054	42.2966	12.2857	79.6823
28	2.136	1.1262	0.0196	1.6277	-0.2736	0.764	-0.1601	-0.0011	0.055	0.1448	0.262	-0.0123	-0.0848	0.0528	-0.034	0.1974	0.0109	0.0183	0.1288	-0.0016	0.157	46.5433	30.0018	76.9344
29	1.7908	0.7546	0.8968	1.6119	0.9676	1.9007	0.1295	-0.2222	-0.1158	0.3129	-0.0387	0.126	0.1819	-0.0707	-0.0461	0.1881	0.0182	0.0174	0.1328	0.0484	0.1131	48.6617	21.4411	74.6307
30	0.4048	-0.324	-0.302	2.8152	1.7383	1.8594	0.0552	-0.3367	0.0256	0.1701	0.0765	-0.2532	-0.0137	-0.0609	-0.0252	0.1836	0.0223	-0.0032	0.1714	0.0163	0.1598	41.4527	33.0442	83.1917
31	1.3005	0.707	0.6227	1.6955	0.644	1.2456	-0.1509	-0.174	0.1993	0.156	0.164	0.0426	-0.2469	0.1121	0.0305	0.2399	0.0095	0.0329	0.1878	-0.0045	0.1929	38.2255	41.3881	81.0656
32	0.3982	-0.342	-0.1772	1.1208	0.103	1.0399	0.0987	-0.0908	-0.007	0.1176	-0.0339	0.1014	-0.0277	0.072	-0.0708	0.1359	-0.0116	0.0235	0.1722	0.0194	0.1732	38.877	30.8032	69.7637

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 15 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 27 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 28 through 47 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 48 through 65 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 66 through 88 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 89 through 100 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 101 through 117 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 118 through 137 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 138 through 161 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 162 through 183 )	A
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 184 through 202 )	A
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 203 through 234 )	A
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 1 through 64 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 65 through 161 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 162 through 234 )	B
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1 through 15 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 16 through 27 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 28 through 63 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 64 through 161 )	C
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 162 through 202 )	C
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 203 through 234 )	C
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 1 through 15 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 16 through 27 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 28 through 65 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 66 through 88 )	D
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 89 through 100 )	D
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 101 through 117 )	D
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 118 through 137 )	D
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 138 through 161 )	D
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 162 through 184 )	D
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 185 through 214 )	D
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 215 through 234 )	D

-
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://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