PDB-4h9z: Structure of Geobacillus kaustophilus lactonase, mutant E101N wit...

ID or keywords:

Entry

Database: PDB / ID: 4h9z

Title

Structure of Geobacillus kaustophilus lactonase, mutant E101N with Mn2+

Components

Phosphotriesterase

Keywords

HYDROLASE / (beta/alpha)8 barrel

Function / homology

Function and homology information

Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / catabolic process / hydrolase activity / zinc ion binding
Similarity search - Function

Biological species

Geobacillus kaustophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.6 Å

Authors

Xue, B. / Chow, J.Y. / Yew, W.S. / Robinson, R.C.

Citation

Journal: Biochemistry / Year: 2013
Title: Structural evidence of a productive active site architecture for an evolved quorum-quenching GKL lactonase.
Authors: Xue, B. / Chow, J.Y. / Baldansuren, A. / Yap, L.L. / Gan, Y.H. / Dikanov, S.A. / Robinson, R.C. / Yew, W.S.

History

Deposition	Sep 25, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 7, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2013	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4h9z.cif.gz	260.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4h9z.ent.gz	221.6 KB	Display	PDB format
PDBx/mmJSON format	4h9z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4h9z_validation.pdf.gz	440.8 KB	Display	wwPDB validaton report
Full document	4h9z_full_validation.pdf.gz	450.9 KB	Display
Data in XML	4h9z_validation.xml.gz	25.2 KB	Display
Data in CIF	4h9z_validation.cif.gz	33.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h9/4h9z ftp://data.pdbj.org/pub/pdb/validation_reports/h9/4h9z	HTTPS FTP

-
Related structure data

Related structure data	4h9tC 4h9uC 4h9vC 4h9xC 4h9yC 4ha0C C: citing same article (ref.)
Similar structure data	6jsu-d 3tn3-d 4h9y-d 4h9u-d 3ojg-1 4wvx-d 3f4d-d 3tnb-d 4ha0-d 6jst-1 6fvp-1 3a3w-1 4ker-2 2r1n-2 4kez-2 4ker-1 3htw-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #158 - Feb 2013 Proton-Gated Urea Channel similarity (1)

Deposited unit

A: Phosphotriesterase

B: Phosphotriesterase

hetero molecules

74 kDa, 2 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)	51.226, 127.817, 51.515
Angle α, β, γ (deg.)	90.000, 95.320, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain 'A' and (resseq 3:99 or resseq 108:144 or resseq...	A	0
2	1	1	chain 'B' and (resseq 3:99 or resseq 108:144 or resseq...	B	0

NCS oper: (Code: given
Matrix: (0.094171, -3.45656), (-4.96797, -1.7219), (-0.995556, 4.66318)
Vector: 46.515301, -66.782402, 51.036598)

#1: Protein	Phosphotriesterase Mass: 36864.914 Da / Num. of mol.: 2 / Mutation: E101N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK1506 / Plasmid: pET-15b, modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5KZU5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.28 Å³/Da / Density % sol: 45.99 %
Crystal grow	Temperature: 293 K / Method: sitting-drop vapor diffusion / pH: 7.5 Details: 100 mM Tris, pH 7.5, 20% (w/v) PEG 4000, 10% (v/v) glycerol, 0.1 mM MnCl2, sitting-drop vapor diffusion, temperature 293K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSRRC

/ Beamline: BL13B1 / Wavelength: 1.311 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 2011

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.311 Å / Relative weight: 1

Reflection

Resolution: 2.3→30 Å / Num. all: 22514 / Num. obs: 22514 / % possible obs: 76.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / R_merge(I) obs: 0.112 / Χ²: 1.012 / Net I/σ(I): 16.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.3-2.34	1.3	0.316	188	1.035	1	12.6
2.34-2.38	1.5	0.251	254	1.008	1	17.5
2.38-2.43	1.7	0.307	362	0.783	1	24.5
2.43-2.48	2	0.248	526	0.782	1	35.5
2.48-2.53	2.1	0.239	660	0.916	1	45.6
2.53-2.59	2.3	0.234	855	0.902	1	57.5
2.59-2.65	2.4	0.215	995	0.934	1	67.6
2.65-2.73	2.6	0.224	1199	0.973	1	80.4
2.73-2.81	2.8	0.206	1281	0.972	1	89
2.81-2.9	2.9	0.192	1426	0.969	1	95.4
2.9-3	3.1	0.154	1479	0.965	1	99.3
3-3.12	3.3	0.15	1443	1.021	1	99.2
3.12-3.26	3.3	0.122	1480	1.02	1	99.7
3.26-3.43	3.4	0.117	1492	1.058	1	99.3
3.43-3.65	3.4	0.11	1476	1.068	1	99.5
3.65-3.93	3.4	0.101	1463	1.07	1	99.7
3.93-4.33	3.4	0.102	1478	1.027	1	99.5
4.33-4.95	3.4	0.105	1469	1.059	1	99.5
4.95-6.23	3.3	0.096	1479	0.87	1	99.3
6.23-30	3.5	0.111	1509	1.17	1	99.4

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 33.27 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3.5 Å	27.14 Å
Translation	3.5 Å	27.14 Å

-
Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHASER	2.1.4	phasing
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.11	data extraction
Blu-Ice		data collection
DENZO		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→19.933 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 0 / Phase error: 24.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2462	929	5.15 %	random
R_work	0.1833	-	-	-
all	0.1866	18030	-	-
obs	0.1866	18030	89.03 %	-

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 17.525 Å² / k_sol: 0.345 e/Å³

Displacement parameters

B_iso max: 109.47 Å² / B_iso mean: 37.5968 Å² / B_iso min: 2.04 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.6444 Å²	0 Å²	-3.3332 Å²
2-	-	-0.7115 Å²	0 Å²
3-	-	-	-2.3168 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→19.933 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5084	0	4	19	5107

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5202
X-RAY DIFFRACTION	f_angle_d	1.162	7040
X-RAY DIFFRACTION	f_chiral_restr	0.076	758
X-RAY DIFFRACTION	f_plane_restr	0.005	930
X-RAY DIFFRACTION	f_dihedral_angle_d	15.539	1928

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	2333	X-RAY DIFFRACTION	POSITIONAL	0.022
1	2	B	2333	X-RAY DIFFRACTION	POSITIONAL	0.022

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.6-2.7368	0.2954	83	0.236	1520	1603	56
2.7368-2.9077	0.3694	106	0.2396	2089	2195	76
2.9077-3.1315	0.2918	141	0.2099	2543	2684	93
3.1315-3.4451	0.2734	146	0.1934	2747	2893	99
3.4451-3.9403	0.2105	143	0.159	2732	2875	100
3.9403-4.9518	0.1903	164	0.1459	2705	2869	99
4.9518-19.9334	0.2481	146	0.1905	2765	2911	99

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	0.086	0.0112	0.0993	0.0738	-0.0058	0.12	0.0233	0.1361	0.0361	-0.0424	-0.0192	0.0191	-0.0243	-0.0836	0.0043	0.0529	0.2091	-0.0844	0.4926	0.0472	0.064	2.7096	-23.9008	7.2787
2	0.1279	0.0823	-0.0585	0.1919	0.0863	0.1431	0.0694	0.0201	0.1158	-0.0396	0.0198	0.1252	-0.1834	-0.1231	0.0763	0.0365	0.2635	-0.042	-0.2189	0.0171	0.0733	24.5248	-23.0927	19.613
3	0.043	-0.0688	-0.0564	0.1094	0.0902	0.074	-0.0045	-0.0274	0.0173	0.0384	0.0006	0.0226	-0.0336	-0.036	0.0055	0.14	0.0432	0.085	0.1249	-0.1241	0.1859	17.994	-20.2147	29.5596
4	0.0225	-0.0063	-0.0081	0.025	0.003	0.0028	0.0174	-0.0277	0.0859	0.0076	0.0051	-0.008	-0.0598	-0.025	0.0079	0.3917	0.2757	0.065	0.1892	-0.1462	0.4357	11.6445	-11.3154	19.3752
5	0.8167	0.2124	-0.0937	0.3203	0.4782	0.9621	-0.0338	0.1575	0.1745	-0.0164	-0.0704	0.0294	-0.1853	-0.2677	-0.1758	0.0037	0.114	-0.1018	0.1468	0.0615	0.1067	15.5582	-24.2196	14.6923
6	0.0301	0.0106	0.0281	0.0271	-0.0198	0.0646	-0.0077	-0.0382	0.0074	0.0279	0.0117	0.0111	-0.0238	-0.0222	-0.0726	0.2029	0.0904	0.1502	0.3286	-0.0429	0.1418	6.7052	-22.1122	22.398
7	0.2676	0.0307	0.2626	0.0912	0.1628	0.5812	-0.0762	-0.0525	0.0971	-0.0661	-0.1022	0.045	-0.1012	-0.1594	-0.5455	0.1222	0.169	0.0699	0.136	-0.1075	0.0586	22.3709	-29.7783	12.1043
8	0.0606	-0.0165	0.0167	0.0042	-0.0049	0.0045	-0.0641	0.0939	0.0233	-0.0022	-0.0339	-0.0289	-0.0113	0.0197	-0.0307	0.0697	0.0926	0.0107	0.4207	-0.0373	0.3149	31.6037	-45.8003	10.6873
9	0.0125	-0.0289	-0.0061	0.0612	0.0118	0.0267	-0.0092	0.0293	-0.05	-0.0203	0.0029	-0.0212	0.0429	-0.0328	0.0925	0.0557	-0.0392	0.2167	0.0161	-0.1364	-0.0726	18.7432	-42.4731	7.8355
10	0.2331	-0.0328	0.2524	0.2087	0.0607	0.3196	-0.0026	-0.1527	-0.022	0.0734	-0.0169	0.045	0.0272	-0.1534	0.1141	-0.1615	-0.0119	0.1186	0.062	0.0498	-0.1286	15.4808	-32.723	10.9733
11	0.0152	0.01	0.026	0.0056	0.0158	0.0441	-0.0185	0.0144	-0.0108	-0.0312	-0.0047	-0.0447	0.0121	0.0466	-0.0513	0.0314	-0.0072	0.0516	0.1651	0.0943	0.0453	35.1461	-32.0428	-0.0624
12	0.153	-0.0712	-0.2887	0.3551	0.2679	0.939	0.0078	0.0842	-0.0142	-0.0527	-0.0833	0.0774	0.0619	-0.2486	-0.2044	0.1105	0.0637	0.0018	0.0806	-0.1024	-0.084	20.1709	-36.873	0.8944
13	1.0051	0.1052	0.5665	0.2688	0.5192	1.1266	-0.0918	0.3545	0.2297	-0.1027	-0.0074	-0.0332	-0.3519	0.0631	-0.3528	0.0557	0.0349	-0.1398	0.1465	0.344	-0.4186	25.2959	-24.4721	-4.5647
14	0.2455	0.0525	-0.1307	0.2312	0.1606	0.2445	0.0243	-0.0105	0.0478	0.1567	0.0207	-0.0613	-0.062	0.0605	0.6667	0.2731	0.1038	-0.1889	0.3103	0.1801	0.0505	25.6862	-17.0409	-0.591
15	0.0351	-0.0233	-0.0178	0.0158	0.0119	0.0091	-0.0266	0.0089	0.0306	-0.0166	0.0074	-0.0314	-0.0151	0.023	0.0083	0.741	0.025	0.0237	0.2698	0.2441	0.5571	28.8938	-6.7627	-0.9593
16	0.0112	0.0082	0.0031	0.0177	0.0344	0.0953	0.0114	0.0761	0.0478	-0.0633	0.0165	0.0378	-0.0798	-0.0166	0.1984	0.4525	0.1363	-0.2818	0.4043	0.2796	0.2716	18.3529	-12.0298	-9.042
17	0.3633	-0.4683	-0.1336	0.7961	-0.061	0.3248	-0.0468	0.0029	0.2048	-0.0697	0.0237	-0.2156	-0.3003	0.0312	0.1851	0.3474	0.0976	-0.0866	-0.0574	-0.0216	0.1165	28.3191	-14.6789	18.1206
18	0.0425	-0.0705	0.002	0.1109	-0.0086	0.0315	0.0236	0.0162	0.0982	-0.0039	0.0419	0.0949	-0.084	-0.0185	0.1159	0.6408	0.1547	-0.0096	0.0429	0.0387	0.5496	22.4775	-5.3908	9.3845
19	0.002	-0.0024	-0.001	0.0046	-0.0023	0.0059	0.0049	-0.0149	0.0093	-0.0392	-0.017	0.0188	-0.0168	-0.0754	-0.0001	0.824	0.1781	0.0467	0.5218	0.2902	0.6302	13.4787	-1.2278	-5.4286
20	0.8958	-0.1563	0.5852	0.1462	-0.1268	0.5144	-0.1013	0.124	0.2585	-0.0062	-0.0495	-0.0679	-0.1315	-0.0254	-0.157	0.1677	0.2542	-0.0553	0.4909	0.1574	0.1889	9.3665	-15.9269	-1.8728
21	0.0581	0.0543	-0.0071	0.0772	-0.0094	0.0016	0.0132	-0.0937	-0.0368	0.0275	-0.0001	-0.0139	0.0317	0.067	0.3534	0.0737	-0.0142	-0.0625	0.5592	0.2539	0.0824	39.4368	-42.885	47.7403
22	0.2151	0.3064	-0.0825	0.5762	0.0624	0.2555	-0.076	-0.1208	-0.2352	0.1881	-0.1205	-0.1406	0.1711	0.0548	-0.6563	0.1218	0.0588	0.0303	-0.221	0.2557	-0.0246	29.2183	-43.6899	24.8445
23	0.0313	0.0507	-0.0158	0.093	-0.0342	0.0143	-0.0124	0.0009	-0.0341	0.0086	0.0101	0.0419	0.0222	-0.0178	0.0222	0.35	-0.1854	0.0004	0.2725	0.0979	0.2819	18.6995	-46.5657	30.4187
24	0.003	0.0087	-0.001	0.0283	0.01	0.0235	0.0032	-0.0378	-0.0675	0.0138	-0.0118	-0.0249	0.093	-0.018	0.0318	0.305	-0.1223	0.0979	0.1495	0.2648	0.3174	28.235	-55.4656	37.7021
25	0.8614	0.3537	-0.2856	0.2695	0.0862	0.4202	0.0411	-0.2263	-0.1976	0.0361	-0.0585	-0.0452	0.1523	0.1262	-0.2163	0.0735	0.0996	-0.1012	0.0963	0.1105	0.0029	33.2698	-42.5628	34.2458
26	0.3162	-0.0308	-0.1426	0.0175	0.0729	0.2975	-0.0374	-0.0237	-0.0568	0.0053	0.0018	0.0112	0.062	-0.0312	-0.0298	0.0426	-0.0324	0.0765	0.3452	0.0974	0.0613	24.7622	-44.6665	42.3379
27	0.1622	0.0299	-0.0896	0.3146	-0.0214	0.1145	0.0772	-0.1092	-0.0713	-0.0875	-0.0341	-0.0387	0.0342	0.0092	0.357	0.0769	-0.0945	0.1942	0.1222	0.1306	0.0507	36.4871	-37.0338	27.7192
28	0.0081	-0.0108	-0.0206	0.0541	-0.0284	0.1256	0.0028	0.0009	-0.0031	-0.0336	0.0064	0.0074	0.0457	0.0844	0.0532	0.2911	-0.1138	0.0318	0.4252	0.105	0.14	38.7673	-20.9824	18.6433
29	0.0984	-0.0008	-0.0111	0.0353	0.0165	0.0096	0.0585	-0.0519	0.0808	-0.0445	0.0084	-0.0514	-0.1034	0.0438	-0.032	0.0658	-0.1278	0.1979	0.0971	-0.0821	0.0985	40.3962	-24.3149	31.7205
30	0.2337	0.0374	0.241	0.1258	0.0536	0.3023	0.0223	-0.1562	0.0205	0.0338	-0.0287	0.0757	0.0089	-0.2085	-0.0409	-0.0816	-0.0002	0.1155	0.1327	-0.0105	-0.127	36.9601	-34.0671	34.6839
31	0.1099	0.0846	0.0048	0.1677	0.0289	0.0061	-0.0163	0.044	-0.0199	-0.0359	0.0306	-0.034	-0.0106	0.0092	-0.0048	0.0868	0.0671	0.0321	0.1316	0.0132	0.0754	49.7937	-34.7441	16.1292
32	0.6461	0.0124	-0.102	0.1328	-0.0082	0.0922	0.0571	-0.2337	0.0238	0.1137	-0.0634	-0.1409	-0.0007	0.0647	0.1114	-0.1012	-0.1709	-0.177	0.0285	-0.0317	0.024	47.4322	-29.91	30.9516
33	0.369	0.183	0.3583	0.1084	0.0979	0.584	0.0938	-0.0121	-0.3345	-0.0241	-0.0017	-0.1238	0.2415	0.2762	-0.6612	-0.4623	0.2309	-0.3517	0.2024	0.0344	0.0122	53.3473	-42.3108	26.359
34	0.1151	0.1401	-0.0578	0.2944	0.0939	0.2953	-0.0208	0.1129	-0.0641	-0.1019	-0.0786	0.1379	0.0469	-0.0042	-0.7961	0.0472	0.1886	-0.2139	0.3652	0.1315	0.3426	49.4542	-49.7409	25.579
35	0.0173	0.0182	-0.0185	0.0192	-0.0193	0.0197	0.0136	0.0209	-0.0282	-0.0076	0.0133	-0.0592	0.0285	0.0142	-0.0028	0.4591	0.1949	0.0426	0.184	0.0913	0.6628	50.1025	-60.0219	22.4397
36	0.0446	0.0066	-0.0321	0.0011	-0.005	0.026	0.0282	0.0123	-0.0802	-0.0005	-0.0212	-0.0492	0.0483	0.065	-0.0731	0.252	0.2646	-0.2793	0.4057	0.175	0.4898	57.1557	-54.7554	33.6981
37	0.1003	-0.177	0.0629	0.7153	-0.5198	0.4682	0.0029	-0.003	-0.2103	-0.1913	-0.0352	-0.0964	0.191	0.048	-0.2756	0.0955	0.0217	-0.1017	-0.0265	0.1589	0.3447	31.1297	-52.1614	21.2748
38	0.039	-0.0508	0.0306	0.0812	-0.0543	0.0357	-0.0478	-0.0088	-0.0878	0.1138	0.0341	0.0724	0.1477	0.0081	-0.0396	0.4991	0.062	-0.0353	0.1187	0.1959	0.7111	39.1545	-61.4009	27.8719
39	0.0805	0.0873	-0.0272	0.1014	-0.0186	0.0291	-0.0229	-0.0389	0.0145	0.034	0.0219	0.0057	0.0002	-0.0115	-0.0058	0.5736	0.2662	-0.0193	0.4457	0.1872	0.8415	53.1026	-65.5526	38.2125
40	0.0623	-0.0158	0.1192	0.1064	-0.0418	0.3622	0.1281	-0.0428	-0.1009	0.0099	-0.0043	-0.0038	0.2847	0.0647	0.0401	0.1837	0.0935	-0.0609	0.4103	0.2523	0.1611	49.1709	-50.8549	41.9692

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 3:19)	A	3 - 19
2	X-RAY DIFFRACTION	2	(chain A and resid 20:41)	A	20 - 41
3	X-RAY DIFFRACTION	3	(chain A and resid 42:47)	A	42 - 47
4	X-RAY DIFFRACTION	4	(chain A and resid 48:61)	A	48 - 61
5	X-RAY DIFFRACTION	5	(chain A and resid 62:81)	A	62 - 81
6	X-RAY DIFFRACTION	6	(chain A and resid 82:87)	A	82 - 87
7	X-RAY DIFFRACTION	7	(chain A and resid 88:109)	A	88 - 109
8	X-RAY DIFFRACTION	8	(chain A and resid 110:114)	A	110 - 114
9	X-RAY DIFFRACTION	9	(chain A and resid 115:131)	A	115 - 131
10	X-RAY DIFFRACTION	10	(chain A and resid 132:149)	A	132 - 149
11	X-RAY DIFFRACTION	11	(chain A and resid 150:155)	A	150 - 155
12	X-RAY DIFFRACTION	12	(chain A and resid 156:175)	A	156 - 175
13	X-RAY DIFFRACTION	13	(chain A and resid 176:217)	A	176 - 217
14	X-RAY DIFFRACTION	14	(chain A and resid 218:240)	A	218 - 240
15	X-RAY DIFFRACTION	15	(chain A and resid 241:248)	A	241 - 248
16	X-RAY DIFFRACTION	16	(chain A and resid 249:262)	A	249 - 262
17	X-RAY DIFFRACTION	17	(chain A and resid 263:282)	A	263 - 282
18	X-RAY DIFFRACTION	18	(chain A and resid 283:302)	A	283 - 302
19	X-RAY DIFFRACTION	19	(chain A and resid 303:310)	A	303 - 310
20	X-RAY DIFFRACTION	20	(chain A and resid 311:325)	A	311 - 325
21	X-RAY DIFFRACTION	21	(chain B and resid 3:19)	B	3 - 19
22	X-RAY DIFFRACTION	22	(chain B and resid 20:41)	B	20 - 41
23	X-RAY DIFFRACTION	23	(chain B and resid 42:47)	B	42 - 47
24	X-RAY DIFFRACTION	24	(chain B and resid 48:61)	B	48 - 61
25	X-RAY DIFFRACTION	25	(chain B and resid 62:81)	B	62 - 81
26	X-RAY DIFFRACTION	26	(chain B and resid 82:87)	B	82 - 87
27	X-RAY DIFFRACTION	27	(chain B and resid 88:109)	B	88 - 109
28	X-RAY DIFFRACTION	28	(chain B and resid 110:114)	B	110 - 114
29	X-RAY DIFFRACTION	29	(chain B and resid 115:131)	B	115 - 131
30	X-RAY DIFFRACTION	30	(chain B and resid 132:149)	B	132 - 149
31	X-RAY DIFFRACTION	31	(chain B and resid 150:155)	B	150 - 155
32	X-RAY DIFFRACTION	32	(chain B and resid 156:175)	B	156 - 175
33	X-RAY DIFFRACTION	33	(chain B and resid 176:217)	B	176 - 217
34	X-RAY DIFFRACTION	34	(chain B and resid 218:240)	B	218 - 240
35	X-RAY DIFFRACTION	35	(chain B and resid 241:248)	B	241 - 248
36	X-RAY DIFFRACTION	36	(chain B and resid 249:262)	B	249 - 262
37	X-RAY DIFFRACTION	37	(chain B and resid 263:282)	B	263 - 282
38	X-RAY DIFFRACTION	38	(chain B and resid 283:302)	B	283 - 302
39	X-RAY DIFFRACTION	39	(chain B and resid 303:310)	B	303 - 310
40	X-RAY DIFFRACTION	40	(chain B and resid 311:325)	B	311 - 325

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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