PDB-3utc: Ec_IspH in complex with (E)-4-hydroxybut-3-enyl diphosphate

ID or keywords:

Entry

Database: PDB / ID: 3utc

Title

Ec_IspH in complex with (E)-4-hydroxybut-3-enyl diphosphate

Components

4-hydroxy-3-methylbut-2-enyl diphosphate reductase

Keywords

OXIDOREDUCTASE / iron-sulfur protein / IspH / LytB / isoprenoid biosynthesis / non-mevalonate pathway

Function / homology

Function and homology information

hydroxymethylbutenyl pyrophosphate reductase activity / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase activity / dimethylallyl diphosphate biosynthetic process / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Span, I. / Wang, K. / Wang, W. / Zhang, Y. / Bacher, A. / Eisenreich, W. / Li, K. / Schulz, C. / Oldfield, E. / Groll, M.

Citation

Journal: Nat Commun / Year: 2012
Title: Discovery of acetylene hydratase activity of the iron-sulphur protein IspH.
Authors: Span, I. / Wang, K. / Wang, W. / Zhang, Y. / Bacher, A. / Eisenreich, W. / Li, K. / Schulz, C. / Oldfield, E. / Groll, M.

History

Deposition	Nov 25, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 5, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 19, 2012	Group: Database references
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3utc.cif.gz	274.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3utc.ent.gz	222.7 KB	Display	PDB format
PDBx/mmJSON format	3utc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3utc_validation.pdf.gz	473.5 KB	Display	wwPDB validaton report
Full document	3utc_full_validation.pdf.gz	483.7 KB	Display
Data in XML	3utc_validation.xml.gz	28.8 KB	Display
Data in CIF	3utc_validation.cif.gz	41.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ut/3utc ftp://data.pdbj.org/pub/pdb/validation_reports/ut/3utc	HTTPS FTP

-
Related structure data

Related structure data	3urkC 3utdC 3uv3C 3uv6C 3uv7C 3uwmC 3ke8S 3dnf 3uv8 PDB Unreleased entry S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3szo-2 4h4e-1 3kem-3 4h4c-2 3zgl-2 3t0f-1 3kel-2 3uv7-2 3t0f-2 3f7t-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase

B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase

hetero molecules

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

1

A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase

hetero molecules

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

2

B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.120, 80.790, 112.560
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.99973, 0.010319, 0.020805), (0.010185, 0.999927, -0.006537), (-0.020871, -0.006323, -0.999762)	-65.6545, 0.31672, -0.47874

#1: Protein	4-hydroxy-3-methylbut-2-enyl diphosphate reductase Mass: 35790.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ispH, lytB, yaaE, b0029, JW0027 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue / References: UniProt: P62623, EC: 1.17.1.2
#2: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄
#3: Chemical	ChemComp-0JX / (3E)-4-hydroxybut-3-en-1-yl trihydrogen diphosphate Mass: 248.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₈P₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.23 Å³/Da / Density % sol: 44.77 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M BIS-TRIS, 0.2 M ammonia sulfate, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2010
Radiation	Monochromator: double-crystal fixed-exit monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→24.85 Å / Num. all: 51128 / Num. obs: 50463 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / R_merge(I) obs: 0.07 / Net I/σ(I): 14.8
Reflection shell	Resolution: 1.9→2 Å / R_merge(I) obs: 0.572 / Mean I/σ(I) obs: 3.9 / % possible all: 94.2

-
Processing

Software

Name	Version	Classification
RemDAq		data collection
REFMAC	5.5.0072	refinement
XDS		data reduction
XSCALE		data scaling
REFMAC	5.5.0072	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KE8

3ke8

Resolution: 1.9→24.85 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.945 / SU B: 7.299 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.593 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22726	2524	5 %	RANDOM
R_work	0.14703	-	-	-
obs	0.15098	47938	98.89 %	-
all	-	50462	-	-

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: 35.541 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.19 Å²	0 Å²	0 Å²
2-	-	-1.7 Å²	0 Å²
3-	-	-	1.51 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→24.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4773	0	44	375	5192

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	4903
X-RAY DIFFRACTION	r_angle_refined_deg	1.96	1.977	6644
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.764	5	617
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.047	24.159	226
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.953	15	853
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.745	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.125	0.2	764
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	3672
X-RAY DIFFRACTION	r_rigid_bond_restr	6.613	3	4899
X-RAY DIFFRACTION	r_sphericity_free	24.584	5	119
X-RAY DIFFRACTION	r_sphericity_bonded	16.744	5	5073

LS refinement shell

Resolution: 1.901→1.95 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.264	161	-
R_work	0.157	3033	-
obs	-	-	90.84 %

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	2.6805	-0.1625	0.413	0.6566	0.5314	0.5487	-0.1094	0.1182	0.0708	0.1955	0.1009	-0.0319	0.1385	0.1016	0.0085	0.0664	0.034	-0.0224	0.0536	0.0182	0.086	-8.9435	-8.002	-7.839
2	2.1847	0.1636	1.1173	0.9046	-0.0722	0.599	0.1264	0.0062	-0.1413	-0.0639	-0.0502	-0.0063	0.076	0.0141	-0.0762	0.0345	0.0055	-0.0014	0.0487	-0.016	0.0409	-29.8033	-10.209	-10.8631
3	2.4419	-0.4443	1.3662	2.8402	0.1053	0.8106	0.3186	0.2653	-0.1911	-0.0667	-0.2123	-0.0261	0.1688	0.1251	-0.1063	0.0946	0.0502	-0.0696	0.0433	-0.0299	0.0541	-40.5092	-13.4978	-21.6956
4	2.6603	-1.3609	0.163	3.3557	0.4261	0.1083	0.1053	0.1991	-0.2805	-0.0528	-0.1032	0.1968	0.0034	0.0136	-0.002	0.0502	0.0348	-0.0147	0.0703	-0.0233	0.0398	-26.8124	-10.3835	-21.6884
5	4.7836	-0.9669	2.1903	2.1608	0.5837	1.5398	0.2016	0.7285	-0.1448	-0.3376	-0.123	0.0093	-0.0596	0.3444	-0.0786	0.0909	0.0387	-0.0301	0.1302	-0.0341	0.0247	-37.4981	-9.8868	-27.7891
6	0.2966	0.3052	0.1527	0.5943	0.8532	1.8213	0.0817	0.0365	0.1043	0.0653	-0.0414	0.0799	0.0197	-0.1563	-0.0404	0.0734	0.0424	-0.0215	0.0685	-0.0129	0.0946	-41.1989	-4.7582	-20.7148
7	2.7837	3.0142	1.0827	8.6972	2.8816	4.2319	0.0423	0.024	0.2948	-0.4262	0.084	0.5029	-0.0925	-0.1283	-0.1264	0.0705	0.0195	-0.0498	0.0435	-0.0031	0.1153	-48.5908	-0.2597	-22.6921
8	0.5969	0.5083	-0.4233	0.4343	-0.3619	0.3016	0.0443	0.0068	0.0647	0.0299	0.0068	0.0622	-0.0237	-0.0036	-0.051	0.0404	0.0148	-0.0179	0.0477	-0.0132	0.0613	-39.0542	-0.5658	-11.785
9	1.2605	-2.7245	1.7589	10.6989	-3.0031	5.1126	0.0441	-0.0219	0.1779	0.8687	0.1705	0.4917	0.1442	-0.2093	-0.2146	0.1914	0.0295	0.194	0.0362	0.0528	0.345	-43.6978	15.3496	-8.9473
10	0.8388	-0.7438	-0.9885	3.0204	0.8161	1.1678	0.0091	-0.003	0.0784	-0.1615	0.0923	0.0543	-0.0083	-0.002	-0.1014	0.0423	0.0204	-0.0114	0.0283	0.0103	0.0395	-31.0703	11.9194	-17.4852
11	0.3287	0.5624	0.0853	1.3412	-0.1854	0.8502	-0.0249	0.0641	0.0794	-0.1345	0.0375	0.2104	-0.1206	-0.0198	-0.0126	0.0947	0.0508	-0.0244	0.0481	0.0069	0.0851	-34.4963	20.9	-16.4452
12	0.5946	-0.0754	-0.0426	1.1001	-0.527	0.2633	-0.0048	-0.0019	0.0263	0.0945	-0.0062	-0.0235	-0.0421	0.0032	0.0109	0.0499	0.009	0.0101	0.0273	-0.0037	0.0405	-24.0259	14.3183	-10.2983
13	2.1308	0.9979	-0.2566	4.8725	-2.8502	1.7233	0.1691	-0.0491	0.2459	0.099	-0.0909	0.1993	-0.0276	0.0535	-0.0782	0.0736	0.0239	0.0193	0.0227	-0.0144	0.0371	-29.1741	22.8539	-5.5254
14	0.4586	-0.3881	-0.4064	0.3787	0.2065	0.8121	0.0205	-0.0081	0.0578	-0.0082	-0.0153	-0.0558	-0.0027	0.0266	-0.0052	0.0511	-0.0131	-0.0005	0.0434	-0.0104	0.0552	-19.2163	2.8642	-5.9283
15	0.6501	0.2564	-0.1905	0.2145	0.1189	0.4172	0.0149	0.0138	-0.0599	-0.0412	0.0037	-0.0688	-0.0567	-0.0247	-0.0186	0.0621	0.0045	0.0372	0.0291	-0.0068	0.0852	-11.4457	0.3004	-16.0549
16	3.9165	1.296	2.4035	1.9116	0.235	3.8158	-0.1046	0.1695	-0.1801	-0.3074	0.065	-0.346	0.1088	0.2519	0.0396	0.0618	0.0111	0.0623	0.0493	-0.0091	0.0765	-2.5555	-8.6127	-20.9527
17	0.1199	0.0562	-0.0967	0.6917	-0.0031	0.0899	-0.003	-0.0073	0.0189	0.0297	0.0091	-0.0671	0.0251	-0.0009	-0.0061	0.063	0.0094	0.011	0.036	-0.013	0.0634	-14.6848	-11.7839	-13.8208
18	1.2223	-0.1484	-0.4186	1.4492	0.6559	1.4014	-0.0172	-0.1262	-0.0763	0.2072	0.0834	-0.2186	0.3128	0.0796	-0.0662	0.0797	0.0191	-0.0252	0.0362	0.0159	0.0589	-7.4273	-11.9138	-7.911
19	1.2788	-0.3928	0.1385	0.1819	-0.3101	1.1858	-0.1959	-0.0003	0.0558	0.0593	0.0095	-0.0573	-0.0212	-0.0252	0.1864	0.0566	-0.0138	-0.009	0.0379	0.0081	0.0416	-31.5626	-7.3373	-2.0697
20	6.3676	-9.6783	-5.6097	22.2225	5.2794	6.3478	-0.2329	-0.1756	-0.4251	0.6148	-0.2112	0.5239	0.107	0.3514	0.4441	0.0425	-0.04	0.0153	0.1014	-0.0254	0.0898	-43.6979	-14.3034	-7.9933
21	0.183	-0.3174	0.2358	0.5977	-0.4471	0.3374	-0.0044	-0.0474	-0.0108	-0.056	0.059	0.0725	0.0539	-0.0538	-0.0546	0.0905	-0.0067	-0.0349	0.0509	-0.0351	0.0892	-56.5567	-7.8157	8.6461
22	0.792	-0.5498	0.4742	0.4856	-0.184	0.5208	0.0316	0.0004	-0.0374	0.0365	0.0107	0.006	0.0998	-0.0144	-0.0424	0.0649	-0.0107	-0.026	0.0327	0.0014	0.034	-33.3193	-11.1273	18.0001
23	2.3628	1.6006	-1.0672	2.5814	-3.3787	5.31	0.238	-0.026	-0.5063	0.0999	0.0571	-0.1347	0.0706	-0.3334	-0.2951	0.1153	-0.0474	-0.0984	0.1847	0.1636	0.2526	-33.2438	-17.9313	25.6424
24	0.5443	-0.174	0.5963	0.6113	-0.3774	0.7259	0.0334	0.0026	0.0037	0.0539	-0.0211	-0.0042	0.0248	0.0271	-0.0123	0.0505	-0.0003	-0.0388	0.0409	-0.0193	0.0453	-24.4599	-5.8764	24.971
25	1.7443	-1.2981	1.2662	3.628	-1.5718	3.4867	-0.0737	0.1299	0.0896	0.089	-0.0665	-0.2875	-0.1711	0.1441	0.1402	0.0358	-0.0234	-0.0449	0.0355	0.0054	0.1027	-17.9216	2.2278	20.7706
26	0.6426	-0.5989	0.6321	0.5644	-0.6146	0.9414	-0.0599	-0.0016	0.0819	0.0588	0.017	-0.0749	0.018	-0.0104	0.0429	0.0568	0.0089	-0.0275	0.0477	-0.0036	0.0437	-22.8367	-4.0473	15.801
27	2.2118	-0.2776	-1.1719	5.5492	2.4736	1.6029	0.2131	0.0496	0.2269	-0.2133	0.0673	-0.412	-0.1864	-0.001	-0.2804	0.0369	-0.0127	0.0079	0.023	0.0302	0.1503	-23.4126	12.285	8.8702
28	0.9057	0.5208	-0.7934	2.0998	-0.7843	1.6243	-0.0127	-0.0479	0.1388	0.1557	0.096	-0.1972	0.0004	-0.0993	-0.0833	0.0515	-0.0061	-0.0311	0.0337	-0.0231	0.0645	-32.7024	13.3861	16.8423
29	2.572	2.7312	-0.4913	5.4797	0.2985	0.5621	-0.016	-0.2837	0.1228	0.1121	0.0621	-0.2831	0.1222	0.1541	-0.0461	0.0817	-0.008	-0.0384	0.0941	-0.0513	0.191	-23.4592	15.1338	17.8963
30	0.9848	0.32	-0.0959	1.4426	-0.0757	0.5268	0.0711	0.004	0.1347	0.1011	-0.0365	-0.0764	-0.0408	-0.0675	-0.0346	0.0515	-0.0011	0.0138	0.011	0.0024	0.061	-37.3611	19.9197	13.5575
31	2.8073	-0.2008	0.1364	1.9733	1.3705	0.9796	0.1809	-0.0084	0.19	-0.1391	-0.0926	-0.1608	-0.0769	-0.0688	-0.0883	0.0851	-0.0113	0.0153	0.0149	0.0235	0.0651	-35.985	22.9866	5.4614
32	0.629	0.9791	-0.2206	1.8082	-0.0725	0.343	-0.0024	0.0024	0.0076	-0.0683	-0.0207	0.0255	-0.0439	-0.0199	0.0232	0.059	0.0026	-0.0027	0.0291	0.0134	0.0373	-44.0576	3.3176	6.2718
33	7.0213	-0.4435	-4.0952	0.1377	-0.0414	3.2942	0.2338	0.2382	0.174	-0.0818	-0.0035	0.0727	0.0709	-0.1598	-0.2302	0.0559	-0.0064	-0.021	0.0489	0.0013	0.179	-60.3808	0.3564	8.5992
34	1.0913	-0.578	-0.0224	0.3452	-0.0928	0.3711	-0.0943	-0.0567	-0.0349	0.1064	0.0341	0.0236	-0.0952	0.0386	0.0602	0.1119	0.0061	0.0393	0.0365	0.0158	0.0605	-48.9934	0.4955	17.8489
35	1.0176	-1.2344	-0.1313	3.9723	-0.177	0.1019	0.022	-0.0254	0.0174	0.1719	-0.008	0.1695	-0.0091	-0.0307	-0.014	0.033	-0.0196	0.0361	0.0447	-0.0065	0.0498	-56.3765	-0.2355	18.7104
36	2.6384	-2.2328	1.9558	2.0403	-1.0348	4.1833	-0.2859	-0.1121	-0.1788	0.318	0.0594	0.2568	0.1114	-0.2523	0.2265	0.0779	-0.0253	0.0716	0.0645	-0.0059	0.1165	-63.6653	-7.9418	21.8522
37	0.5544	-0.0124	-0.4313	0.369	0.1722	0.6612	0.0121	0.0931	-0.0024	0.0839	-0.0151	0.0767	0.0552	0.0505	0.003	0.0441	0.0021	-0.0056	0.0879	-0.0042	0.0634	-50.7579	-11.3961	14.3758
38	2.6331	0.6751	-1.1162	3.0481	-1.9412	1.8547	0.0251	0.233	-0.1348	-0.226	0.0658	0.4124	0.1769	-0.0807	-0.0909	0.041	-0.0148	-0.0158	0.0452	-0.016	0.1077	-57.9311	-11.6052	8.7332
39	3.5934	-0.2773	1.6149	0.0401	0.0195	1.8836	-0.135	0.1774	0.0063	0.0246	-0.0019	0.0145	0.0021	0.1616	0.1369	0.0646	0.0041	-0.0059	0.0341	-0.0033	0.0286	-32.898	-7.6532	3.1293
40	10.3133	-6.759	-6.9693	20.6785	-6.2952	11.9717	-0.0702	0.1612	0.002	-0.7255	-0.235	-0.43	0.579	-0.0134	0.3052	0.1277	0.0773	-0.0137	0.0639	-0.0189	0.0333	-22.3276	-15.6594	7.8487

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 7
2	X-RAY DIFFRACTION	2	A	8 - 24
3	X-RAY DIFFRACTION	3	A	25 - 37
4	X-RAY DIFFRACTION	4	A	38 - 49
5	X-RAY DIFFRACTION	5	A	50 - 64
6	X-RAY DIFFRACTION	6	A	65 - 77
7	X-RAY DIFFRACTION	7	A	78 - 89
8	X-RAY DIFFRACTION	8	A	90 - 103
9	X-RAY DIFFRACTION	9	A	104 - 114
10	X-RAY DIFFRACTION	10	A	115 - 127
11	X-RAY DIFFRACTION	11	A	128 - 162
12	X-RAY DIFFRACTION	12	A	163 - 181
13	X-RAY DIFFRACTION	13	A	182 - 193
14	X-RAY DIFFRACTION	14	A	194 - 210
15	X-RAY DIFFRACTION	15	A	211 - 246
16	X-RAY DIFFRACTION	16	A	247 - 261
17	X-RAY DIFFRACTION	17	A	262 - 280
18	X-RAY DIFFRACTION	18	A	281 - 297
19	X-RAY DIFFRACTION	19	A	298 - 304
20	X-RAY DIFFRACTION	20	A	305 - 309
21	X-RAY DIFFRACTION	21	B	1 - 7
22	X-RAY DIFFRACTION	22	B	8 - 49
23	X-RAY DIFFRACTION	23	B	50 - 54
24	X-RAY DIFFRACTION	24	B	55 - 76
25	X-RAY DIFFRACTION	25	B	77 - 86
26	X-RAY DIFFRACTION	26	B	87 - 100
27	X-RAY DIFFRACTION	27	B	101 - 112
28	X-RAY DIFFRACTION	28	B	113 - 127
29	X-RAY DIFFRACTION	29	B	128 - 140
30	X-RAY DIFFRACTION	30	B	141 - 181
31	X-RAY DIFFRACTION	31	B	182 - 193
32	X-RAY DIFFRACTION	32	B	194 - 207
33	X-RAY DIFFRACTION	33	B	208 - 216
34	X-RAY DIFFRACTION	34	B	217 - 235
35	X-RAY DIFFRACTION	35	B	236 - 248
36	X-RAY DIFFRACTION	36	B	249 - 261
37	X-RAY DIFFRACTION	37	B	262 - 280
38	X-RAY DIFFRACTION	38	B	281 - 297
39	X-RAY DIFFRACTION	39	B	298 - 305
40	X-RAY DIFFRACTION	40	B	306 - 310

-
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