PDB-4h9t: Structure of Geobacillus kaustophilus lactonase, mutant E101N wit...

ID or keywords:

Entry

Database: PDB / ID: 4h9t

Title

Structure of Geobacillus kaustophilus lactonase, mutant E101N with bound N-butyryl-DL-homoserine lactone

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: 2.097 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 24, 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	4h9t.cif.gz	268.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4h9t.ent.gz	228.2 KB	Display	PDB format
PDBx/mmJSON format	4h9t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4h9t_validation.pdf.gz	462.6 KB	Display	wwPDB validaton report
Full document	4h9t_full_validation.pdf.gz	465 KB	Display
Data in XML	4h9t_validation.xml.gz	27.9 KB	Display
Data in CIF	4h9t_validation.cif.gz	39.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h9/4h9t ftp://data.pdbj.org/pub/pdb/validation_reports/h9/4h9t	HTTPS FTP

-
Related structure data

Related structure data	4h9uC 4h9vC 4h9xC 4h9yC 4h9zC 4ha0C C: citing same article (ref.)
Similar structure data	4h9y-d 1p6c-d 6jsu-d 4ker-1 3a3w-1 3gtf-1 6fev-d 2r1k-2 4h9u-d 3f4d-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

-
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

74.3 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)	78.231, 91.419, 95.686
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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: (-0.983795, -0.151463, -0.09595), (-0.158389, 0.483362, 0.860973), (-0.084027, 0.862218, -0.499519)
Vector: 23.1803, 33.719799, -53.832298)

#1: Protein	Phosphotriesterase Mass: 36863.930 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: Chemical	ChemComp-HL4 / N-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide / N-butyryl-L-homoserine lactone Mass: 171.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₃NO₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.32 Å³/Da / Density % sol: 46.99 %
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, 1.0mM N-butyryl-DL-homoserine lactone, sitting-drop vapor diffusion, temperature 293K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSRRC

/ Beamline: BL13B1 / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2011

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.097→30 Å / Num. all: 40871 / Num. obs: 40871 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / R_merge(I) obs: 0.052 / Χ²: 0.978 / Net I/σ(I): 14.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.1-2.14	5.3	0.443	2026	0.954	1	99.6
2.14-2.18	5.8	0.4	1992	0.938	1	99.8
2.18-2.22	6	0.336	1989	0.942	1	99.8
2.22-2.26	6.1	0.299	2027	1.007	1	100
2.26-2.31	6.1	0.258	2016	0.925	1	100
2.31-2.37	6.2	0.236	2026	0.94	1	100
2.37-2.42	6.1	0.191	2018	0.955	1	100
2.42-2.49	6.1	0.163	2021	0.962	1	100
2.49-2.56	6.1	0.14	2022	0.958	1	100
2.56-2.65	6.1	0.117	2022	0.953	1	99.9
2.65-2.74	6.1	0.1	2033	0.968	1	100
2.74-2.85	6.1	0.083	2025	0.947	1	100
2.85-2.98	6.1	0.065	2043	0.933	1	100
2.98-3.14	6.1	0.05	2046	0.926	1	99.9
3.14-3.33	6.1	0.041	2046	0.906	1	100
3.33-3.59	6	0.041	2060	1.121	1	100
3.59-3.95	5.9	0.041	2069	1.532	1	100
3.95-4.52	5.9	0.036	2076	1.333	1	100
4.52-5.69	5.7	0.026	2106	0.739	1	99.6
5.69-30	5.7	0.022	2208	0.613	1	99.5

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 42.69 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3.5 Å	33.66 Å
Translation	3.5 Å	33.66 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: 2.097→19.941 Å / Occupancy max: 1 / Occupancy min: 0.61 / SU ML: 0.23 / σ(F): 0 / Phase error: 21.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2096	2016	5.02 %	random
R_work	0.1826	-	-	-
all	0.184	40173	-	-
obs	0.184	40173	98.32 %	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 26.962 Å² / k_sol: 0.335 e/Å³

Displacement parameters

B_iso max: 98.73 Å² / B_iso mean: 28.2997 Å² / B_iso min: 3.9 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.7195 Å²	0 Å²	0 Å²
2-	-	5.6751 Å²	-0 Å²
3-	-	-	3.8215 Å²

Refinement step

Cycle: LAST / Resolution: 2.097→19.941 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5034	0	28	341	5403

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5174
X-RAY DIFFRACTION	f_angle_d	1.022	6998
X-RAY DIFFRACTION	f_chiral_restr	0.069	756
X-RAY DIFFRACTION	f_plane_restr	0.005	918
X-RAY DIFFRACTION	f_dihedral_angle_d	14.361	1916

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	0.038
1	2	B	2333	X-RAY DIFFRACTION	POSITIONAL	0.038

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.097-2.1494	0.2569	112	0.2081	2170	2282	80
2.1494-2.2074	0.2369	128	0.2099	2678	2806	97
2.2074-2.2723	0.2725	132	0.2035	2739	2871	100
2.2723-2.3455	0.2659	150	0.1982	2722	2872	100
2.3455-2.4292	0.2402	130	0.204	2751	2881	100
2.4292-2.5263	0.2762	128	0.1917	2792	2920	100
2.5263-2.641	0.2178	146	0.1938	2725	2871	100
2.641-2.7799	0.2453	138	0.1945	2740	2878	100
2.7799-2.9536	0.2393	165	0.1972	2771	2936	100
2.9536-3.1808	0.1919	136	0.1831	2774	2910	100
3.1808-3.4993	0.2122	162	0.1881	2766	2928	100
3.4993-4.0021	0.2067	162	0.1705	2789	2951	100
4.0021-5.0288	0.1444	153	0.1463	2821	2974	100
5.0288-19.9422	0.1928	174	0.1812	2919	3093	100

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	0.1313	0.1704	0.1367	0.4423	0.1726	0.5834	-0.0146	0.0291	-0.0036	-0.1059	-0.0055	0.2521	0.1041	-0.1236	0.0087	0.1495	-0.0751	-0.1043	0.0521	0.0105	0.2096	-15.9897	5.3318	-30.1253
2	1.066	0.2872	-0.0424	0.4126	-0.1612	0.379	-0.0503	0.0386	-0.0134	0.0481	-0.0611	-0.1397	-0.1322	0.329	0.1282	0.1749	-0.1357	-0.0078	0.1755	0.0296	0.1041	5.8839	10.9675	-19.4962
3	8.4035	3.3959	-4.9713	1.9458	-2.1853	3.6442	0.0695	-0.0674	-0.2147	0.028	-0.0756	-0.4763	0.025	0.48	-0.0291	0.216	0.0215	-0.001	0.125	-0.0171	0.2909	9.8271	-0.5673	-21.8435
4	2.9141	0.8602	-1.4167	0.6193	-0.1135	1.7302	-0.0648	-0.1825	-0.3421	0.2834	-0.017	0.2025	0.343	-0.0726	-0.0014	0.3082	-0.0328	-0.0152	0.1224	0.0671	0.3086	-4.3659	-2.7781	-15.8834
5	0.4383	0.0248	-0.2046	0.5892	0.0344	0.7067	0.1002	-0.0305	-0.1958	0.085	-0.0553	0.0596	0.1213	0.0133	0.017	0.0802	-0.0132	-0.0468	0.017	0.0039	0.1002	-2.6446	8.7802	-24.4332
6	0.3238	0.6235	-0.1344	1.3604	-0.3463	0.6059	-0.0035	0.0216	-0.1622	-0.1726	0.1342	-0.3272	0.33	0.0792	-0.0434	0.2883	0.0196	-0.0655	0.0393	-0.0629	0.1942	-2.3472	-2.4994	-28.2715
7	0.7618	0.415	-0.2588	0.5928	-0.1141	0.4788	0.1971	-0.0555	-0.004	0.1326	-0.0445	-0.0338	-0.1003	0.0597	0.075	0.1117	-0.0515	-0.0052	0.0066	-0.0174	0.1371	-0.2264	16.4795	-25.9992
8	1.9469	-0.0043	0.7791	2.9647	1.2089	3.7996	-0.0296	-0.1977	0.3104	0.1562	0.0448	-0.0675	-0.3501	0.0671	-0.0203	0.3812	-0.0735	-0.0388	0.2578	0.0979	0.2683	8.6203	32.4284	-33.0647
9	0.3282	-0.1976	0.1987	0.8507	-0.4978	0.6318	-0.0173	0.1061	0.1322	-0.112	-0.0627	-0.1054	-0.1227	0.092	-0.0322	0.0668	0.0173	-0.0219	-0.0053	0.1468	0.0227	-2.1063	24.3976	-36.7475
10	0.7376	-0.0278	-0.0859	1.411	0.3052	1.0275	0.0181	0.029	-0.0527	0.002	0.0441	-0.1144	0.0664	0.0497	-0.1113	0.1056	-0.0338	0.0013	-0.038	-0.0481	0.0231	-3.5975	15.5996	-31.0798
11	0.3862	0.2792	0.0371	0.9864	-0.1831	1.9878	0.0285	-0.0457	0.0542	0.0926	-0.0515	-0.0376	-0.2707	0.1671	0.036	0.2437	-0.1595	-0.0049	0.1041	-0.0337	0.1502	-2.0315	34.6734	-18.4909
12	0.3425	0.5037	0.0751	1.4836	-0.0278	0.3981	-0.0367	0.0829	0.1892	-0.1669	0.0077	0.1271	-0.158	-0.0098	0.1299	0.0614	0.0251	-0.0416	-0.1397	0.1012	0.0776	-8.1212	26.7332	-30.5141
13	1.5128	0.3246	0.1516	1.372	-0.0223	0.9001	0.0914	-0.3359	0.3573	0.1212	-0.0224	0.1645	-0.2474	-0.0729	0.0981	0.0789	0.0169	0.0152	-0.0055	-0.0723	0.1752	-12.4761	26.8241	-16.7294
14	0.9796	-0.655	-0.4048	1.6021	-0.8647	1.2652	-0.0808	-0.2865	0.2477	0.1716	0.0242	-0.241	-0.0998	0.0977	0.0288	-0.0077	0.0574	0.0468	0.0485	-0.0807	0.1405	-10.654	20.9713	-10.2829
15	1.7151	-0.5674	-0.1919	0.3334	0.0787	0.8359	0.0089	-0.2654	0.091	0.2208	0.0526	0.0249	-0.1338	0.0467	0.0222	0.2268	0.042	0.0677	0.3433	-0.0628	0.1047	-11.6711	17.6454	-0.6385
16	1.0497	-0.403	-0.3585	0.7585	-0.4847	2.7257	0.0008	-0.1793	0.0898	0.1111	0.0578	0.2136	-0.051	-0.295	0.009	0.099	-0.0114	0.0818	0.24	-0.0145	0.2384	-22.6634	18.508	-9.3163
17	1.2195	-0.1678	-0.3161	0.4517	0.0351	0.4699	-0.0815	-0.4832	0.0758	0.2942	0.0361	-0.1525	-0.0141	0.2997	-0.0121	0.145	-0.0401	-0.0443	0.2301	0.0088	0.1245	4.8723	9.9072	-9.8766
18	0.4764	0.149	-0.3589	0.482	-0.2659	0.3239	0.0329	-0.2902	-0.1013	0.1057	0.0243	0.0606	0.0078	-0.03	0.1806	0.23	-0.0413	-0.0016	0.3528	0.1145	0.1605	-7.4718	6.8624	-4.1621
19	3.8177	0.4382	-2.1824	2.4475	1.0095	2.286	-0.0161	-0.0545	0.0072	0.1128	-0.0636	0.2114	0.0554	-0.2185	-0.001	0.1742	0.0051	0.1452	0.4043	0.0796	0.2786	-25.1336	8.0568	-3.6769
20	1.358	0.2191	-0.798	0.9517	-0.1519	1.7354	-0.031	-0.0913	-0.0685	-0.018	-0.0089	0.1592	0.1031	-0.2204	-0.0016	0.0632	-0.0451	-0.0052	0.1522	0.0209	0.1942	-21.1099	10.7467	-18.429
21	0.6473	-0.3376	0.5078	2.7484	-1.8466	1.9794	-0.126	-0.1164	-0.1561	0.1326	-0.05	-0.412	0.1791	0.4479	0.0674	0.2266	0.1125	-0.0013	0.4121	0.0628	0.3465	41.0383	12.6665	-32.5432
22	2.1451	0.0501	-0.2297	0.3342	-0.0296	0.3521	0.0148	-0.2102	-0.0148	-0.0021	0.0553	-0.0574	-0.0848	0.101	-0.0191	0.1109	0.0176	0.0342	0.1279	0.0237	0.0894	17.7271	21.2314	-35.0641
23	5.0631	1.5271	-3.5284	6.2494	1.4991	3.5945	-0.0346	0.3262	-0.0372	-0.1744	-0.0124	0.3602	0.1016	-0.4262	-0.0709	0.214	-0.0713	0.0119	0.3205	-0.0976	0.2126	15.8806	13.0236	-44.2006
24	3.8206	2.3728	-2.0576	2.856	-1.1244	1.268	-0.0849	0.2814	-0.0091	-0.1458	0.0648	0.0734	0.0122	-0.1455	0.0056	0.1318	0.0181	0.0692	0.1247	-0.0181	0.0266	29.6992	19.2292	-47.7311
25	0.2229	0.3063	-0.272	0.6778	-0.1509	0.8634	0.0789	-0.1662	-0.1282	0.0727	-0.1073	0.0025	0.1662	0.1048	0.0328	0.122	0.0073	0.0337	0.1852	0.0169	0.1095	26.8793	17.2175	-33.685
26	6.3458	-0.931	-3.52	8.521	-4.3862	8.6325	-0.0077	0.3333	-0.4926	-0.4563	-0.0341	0.3174	0.6853	-0.4473	-0.0047	0.3997	0.0184	0.0067	0.137	-0.0088	0.2687	28.7041	8.3991	-41.5158
27	1.7313	-0.1708	-1.5326	0.6953	0.0446	1.5785	0.2695	-0.1001	0.0338	0.068	-0.2086	-0.0986	-0.1158	-0.0805	-0.063	0.1849	-0.0846	0.0017	0.2671	-0.0275	0.1292	23.4304	19.2247	-26.5046
28	1.9604	-0.7428	-0.0804	3.7922	0.2673	2.4254	-0.0852	-0.1931	0.2806	0.2034	-0.017	0.1424	-0.2789	-0.0511	0.0204	0.6347	-0.1233	0.0024	0.3845	-0.0891	0.2357	12.7854	19.4832	-10.0848
29	0.47	-0.1047	0.0038	0.2557	0.0408	1.1599	-0.0256	-0.2105	-0.0197	0.1843	-0.0106	-0.0526	0.0712	0.0499	-0.0527	0.2558	-0.097	-0.0768	0.5157	0.1248	0.1612	24.935	14.0494	-14.127
30	1.3754	-0.5448	-0.2903	2.3966	0.8232	1.7468	-0.0204	-0.166	-0.1262	0.0283	-0.0892	0.172	0.1456	0.037	0.0524	0.292	-0.0639	0.0114	0.3062	0.0733	0.2112	27.3075	14.9092	-24.4181
31	1.7451	1.046	-1.0805	3.2961	-0.6699	1.5821	0.0567	-0.0467	0.1831	0.3026	0.1559	0.3096	-0.3872	-0.397	-0.1603	0.5386	-0.0815	0.1591	0.7673	-0.0659	0.6611	21.6777	34.7532	-14.412
32	1.0217	-0.5952	-0.5054	0.7174	0.4947	1.9037	-0.011	-0.2084	-0.0415	0.1504	0.0567	-0.0285	0.113	0.0423	0.1109	0.2779	-0.1185	-0.0547	0.5255	0.0696	0.1669	29.9288	21.4706	-14.6595
33	1.5254	0.3308	-0.5695	1.1553	-0.2812	2.4877	0.1851	-0.2983	0.4303	0.1594	0.0124	0.0953	-0.476	0.0564	0.2097	0.3432	-0.2139	0.0118	0.4627	-0.0701	0.2363	33.0458	34.0533	-21.0594
34	0.7053	0.2304	0.6405	0.8827	0.1651	1.5471	0.0917	-0.4175	0.2535	0.1974	-0.1514	-0.0466	-0.2218	0.0033	0.2506	0.3215	-0.1608	0.0942	0.3406	-0.134	0.2203	31.8007	35.8973	-29.4415
35	2.9577	0.9921	1.6126	1.4664	0.2931	1.4382	-0.1501	-0.0213	0.3373	0.0056	-0.0023	0.0218	-0.3066	0.0458	0.008	0.4118	-0.0603	0.1814	0.1775	-0.0611	0.4091	32.3891	43.3803	-37.0908
36	1.0823	0.6507	0.1449	1.5228	-0.505	0.3284	0.0462	-0.0497	0.1327	0.0291	-0.103	-0.2661	-0.1366	0.1977	0.0866	0.3407	-0.2603	0.0963	0.5131	-0.0287	0.3708	43.7805	37.9699	-30.9226
37	1.9735	1.1443	-0.3617	1.0312	0.3166	0.8224	-0.0107	0.2173	0.3297	-0.2475	0.0402	0.0616	-0.3629	-0.1864	-0.0265	0.1819	0.009	0.037	0.2076	0.0028	0.11	18.0321	29.181	-40.5752
38	2.4303	1.0074	0.171	0.4895	0.4004	1.5279	0.0691	0.1131	0.4105	-0.0805	-0.0147	0.1186	-0.3921	-0.093	-0.1075	0.2113	0.0243	0.1209	0.1008	0.0042	0.1395	30.1739	34.4853	-44.9373
39	1.6153	-0.3556	-1.3766	1.6448	-1.4492	3.316	-0.008	0.0444	0.0042	-0.041	-0.0664	-0.301	-0.0346	0.2319	0.1742	0.3565	-0.2208	0.1253	0.4807	0.0031	0.4844	47.3814	38.1598	-42.5033
40	1.3792	0.3807	-0.233	1.1345	-0.3622	0.6848	0.0337	-0.1337	-0.0964	0.0017	-0.0179	-0.2218	0.0001	0.1475	0.1889	0.1625	-0.0653	0.0168	0.5458	0.0235	0.2381	44.2472	26.126	-33.2056

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://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

-
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