PDB-3uwm: Ec_IspH in complex with 4-oxobutyl diphosphate (1302)

ID or keywords:

Entry

Database: PDB / ID: 3uwm

Title

Ec_IspH in complex with 4-oxobutyl diphosphate (1302)

Components

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

Keywords

OXIDOREDUCTASE / Cytosol / iron-sulfur protein / Reductase

Function / homology

Function and homology information

: / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase activity / dimethylallyl diphosphate biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 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: 1.8 Å

Authors

Span, I. / Wang, K. / Wang, W. / Zhang, Y. / Bacher, A. / Eisenreich, W. / 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	Dec 2, 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_alt_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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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	3uwm.cif.gz	279.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3uwm.ent.gz	226.6 KB	Display	PDB format
PDBx/mmJSON format	3uwm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uw/3uwm ftp://data.pdbj.org/pub/pdb/validation_reports/uw/3uwm	HTTPS FTP

-
Related structure data

Related structure data	3urkC 3utcC 3utdC 3uv3C 3uv6C 3uv7C 3ke8S 3dnf S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4h4e-2 3ke8-2 3zgn-1 3utc-2 3utd-1 4muy-1 4h4d-2 3ke9-1 3f7t-1 3szl-2 4mux-1 3uv7-2 3urk-1 3kef-2 3ke8-3 4h4e-1 3kel-3 3szu-1 3zgl-1 3t0g-1 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
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

73.3 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
36.6 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
36.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.660, 80.700, 111.790
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	(-0.999895, 0.004811, 0.01364), (0.004861, 0.999982, 0.003642), (-0.013622, 0.003708, -0.9999)	-66.01871, 0.16199, -0.47989

#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-0K2 / 4-oxobutyl trihydrogen diphosphate Mass: 248.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₈P₂
#4: 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
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 455 / 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: 44.75 %
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
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: 1.8→50 Å / Num. all: 59963 / Num. obs: 59603 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / R_merge(I) obs: 0.096 / Net I/σ(I): 10.9
Reflection shell	Resolution: 1.8→1.9 Å / R_merge(I) obs: 0.371 / Mean I/σ(I) obs: 4.2 / % possible all: 97.6

-
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: 1.8→50 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.926 / SU B: 6.987 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26831	2981	5 %	RANDOM
R_work	0.18459	-	-	-
obs	0.18875	56621	99.45 %	-
all	-	59603	-	-

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: 27.041 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.12 Å²	0 Å²	0 Å²
2-	-	-2.21 Å²	0 Å²
3-	-	-	2.09 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4773	0	72	455	5300

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.019	4895
X-RAY DIFFRACTION	r_angle_refined_deg	2.084	1.974	6626
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.091	5	617
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.575	24.159	226
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.755	15	853
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.002	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.145	0.2	762
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	3664
X-RAY DIFFRACTION	r_rigid_bond_restr	5.865	3	4895
X-RAY DIFFRACTION	r_sphericity_free	29.914	5	132
X-RAY DIFFRACTION	r_sphericity_bonded	19.341	5	5138

LS refinement shell

Resolution: 1.8→1.846 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.313	198	-
R_work	0.178	3678	-
obs	-	-	95.02 %

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	0.0092	0.0127	0.0054	0.0181	0.0071	0.0038	0.0145	-0.0152	-0.023	0.01	-0.0097	-0.0366	0.0117	-0.0094	-0.0048	0.0871	0.001	-0.0082	0.0731	0.0011	0.0935	-12.2539	-6.6686	-9.2054
2	0.49	0.19	0.0582	0.0758	0.0221	0.0071	0.0098	-0.0335	-0.0269	-0.0092	-0.0097	-0.0096	0.0038	-0.0052	-0.0001	0.0787	0.0013	-0.0013	0.0689	-0.0013	0.0803	-29.8363	-10.1741	-11.0324
3	0.4559	0.6063	-0.0827	1.1384	-0.2657	0.1312	0.0412	0.0335	-0.0153	0.004	-0.0357	0.0194	-0.0191	0.005	-0.0054	0.0727	0.0057	-0.0083	0.0734	-0.006	0.0801	-40.2963	-13.4078	-21.8597
4	0.5662	-0.1386	0.1679	0.1865	-0.066	0.4152	0.0135	0.018	-0.0721	0.0136	-0.0042	-0.0032	-0.0267	-0.0012	-0.0093	0.0754	0.0046	-0.0024	0.0657	-0.0007	0.0731	-26.7853	-10.2301	-21.8343
5	0.8342	-0.6716	-0.055	0.6445	0.1417	0.0964	0.0484	0.0525	-0.0101	-0.0522	-0.0312	-0.0216	-0.0152	-0.006	-0.0173	0.0814	0.0103	-0.0035	0.0832	-0.0048	0.079	-37.5153	-9.507	-27.73
6	0.1698	0.2516	0.1042	0.3899	0.1973	0.206	-0.0165	-0.0087	0.0163	-0.0404	-0.0119	0.0374	-0.0034	-0.0037	0.0284	0.0743	0.0069	-0.0042	0.0724	-0.005	0.0829	-41.1928	-4.698	-20.773
7	0.2468	0.6261	0.253	1.74	0.8855	0.6528	-0.017	-0.0053	0.0067	-0.0729	-0.0779	0.0674	-0.0757	-0.104	0.0949	0.0711	0.0099	-0.0207	0.0716	-0.0122	0.0922	-48.5668	-0.1263	-22.6684
8	0.0717	0.1964	-0.007	0.5764	0.0717	0.2369	0.0019	-0.0066	0.0188	0.0008	-0.028	0.0695	0.0029	0.0046	0.0261	0.0722	0.0074	-0.0066	0.0674	0.0049	0.0795	-39.083	-0.4953	-11.8719
9	1.2618	-0.8298	-0.4274	1.3353	-0.5223	0.9636	0.0231	0.0033	0.0506	-0.042	0.0326	0.0223	0.0296	-0.0327	-0.0557	0.0658	0.0018	-0.0134	0.0679	-0.0142	0.108	-43.8565	15.5175	-9.1788
10	0.0285	0.0068	-0.0454	0.3072	0.1186	0.1275	0.0038	0.0017	0.0086	-0.0435	-0.012	0.0497	-0.0181	-0.0088	0.0082	0.0827	0.0048	-0.0037	0.0677	-0.003	0.0823	-31.0781	12.0804	-17.523
11	0.1688	0.0055	-0.059	0.4114	0.0005	0.0209	0.0063	0.0066	0.0129	-0.0609	-0.0046	0.0445	-0.0047	0.0002	-0.0017	0.0838	0.0032	-0.008	0.068	0.0003	0.0792	-34.5869	21.0677	-16.4571
12	0.0616	0.0111	0.0422	0.1586	0.0183	0.0983	0.0096	0.0097	0.0049	-0.0149	-0.0039	-0.0035	-0.0079	0.0007	-0.0057	0.0735	0.0001	0	0.0662	-0.0028	0.0834	-24.129	14.4286	-10.2321
13	0.1926	0.1466	0.009	0.5459	-0.3599	0.3147	0.0058	-0.0058	0.0265	-0.0086	-0.0173	0.0231	0.0116	0.0272	0.0115	0.0769	0.0032	0.0027	0.068	-0.0034	0.0798	-29.3964	22.8788	-5.46
14	0.3697	-0.1383	-0.0928	0.1686	-0.0168	0.0478	0.0076	-0.0428	0.0353	-0.017	0.001	-0.0216	0.0085	0.0078	-0.0086	0.0734	0.0023	-0.003	0.0686	-0.0038	0.0809	-19.4223	2.9237	-5.8853
15	0.2934	0.0424	0.0323	0.1009	0.0572	0.036	-0.0057	0.0111	0.013	-0.015	0.0073	-0.0271	0.0001	-0.0017	-0.0016	0.0773	-0.0001	0.0026	0.0667	0.0015	0.0833	-11.555	0.41	-15.9131
16	0.8643	0.1377	0.1539	0.0295	-0.0604	1.7311	0.0142	0.0239	0.0526	-0.0024	-0.0157	-0.0064	0.1043	0.0806	0.0015	0.0588	0.0132	-0.008	0.0641	0.0101	0.0963	-2.6353	-8.5279	-20.7701
17	0.6292	0.0011	0.0283	0.0028	-0.0162	0.0983	-0.0036	-0.029	0.0049	-0.0054	0.0019	-0.002	0.0253	-0.0062	0.0017	0.0747	0.0024	-0.0013	0.0654	-0.0003	0.085	-14.7936	-11.6681	-13.73
18	0.1495	-0.1368	-0.1577	0.1724	0.0753	0.6073	-0.0036	-0.0261	-0.0191	0	-0.0072	-0.0193	0.0328	-0.0009	0.0108	0.0598	-0.0015	0.0022	0.0711	0.0036	0.088	-7.6587	-11.8236	-7.7642
19	0.5456	0.0046	0.4746	0.0219	0.0935	0.7789	0.0003	-0.0515	-0.0114	0.0048	-0.0024	0.0027	0.0227	-0.0494	0.0021	0.0795	-0.0012	-0.0024	0.0757	0.0004	0.075	-31.7497	-7.3672	-2.2357
20	1.3797	0.6833	0.7467	0.3389	0.3695	0.4047	0.0586	-0.2435	0.0769	0.0236	-0.1156	0.0341	0.0219	-0.1279	0.057	0.07	-0.0239	-0.0015	0.1129	0.0044	0.1079	-43.8039	-14.3679	-8.4656
21	0.2401	0.1651	0.1432	0.1808	0.0661	0.1019	0.0148	0.0433	0.006	-0.0053	0.0038	0.0441	0.0155	0.0316	-0.0187	0.0808	-0.0011	-0.0036	0.0631	-0.0073	0.0782	-53.6692	-6.6481	9.4629
22	0.2089	-0.0994	0.063	0.1702	-0.1011	0.0609	0.0089	-0.0026	-0.0129	0.0099	-0.0108	0.0002	0.0003	0.0023	0.0019	0.0783	-0.0031	-0.0027	0.0682	0.0004	0.0795	-33.747	-11.2314	17.7724
23	2.8258	-0.9423	0.5974	0.3152	-0.1985	0.1277	-0.0114	-0.0504	-0.0599	0.0145	0.0263	0.0136	-0.0048	-0.0065	-0.0149	0.1109	-0.0011	-0.0153	0.0718	0.006	0.0944	-33.6698	-17.9783	25.4754
24	0.3285	-0.0901	0.2367	0.1018	-0.1728	0.3226	0.0203	-0.0169	-0.0072	0.0079	-0.013	0.0025	-0.0087	0.0046	-0.0074	0.0813	-0.0082	-0.0063	0.0698	0.0016	0.0806	-24.9471	-5.8835	24.8218
25	0.0813	0.3912	-0.1389	1.8863	-0.6696	0.2379	0.0089	-0.0117	-0.0314	0.0488	-0.0681	-0.1549	-0.0187	0.022	0.0592	0.0782	-0.0103	-0.0116	0.0708	0.0082	0.1006	-18.4414	2.2448	20.8519
26	0.0068	-0.0159	0.0302	0.0452	-0.0495	0.4064	0.0051	0.0211	0.0108	-0.016	-0.0406	-0.0456	0.0247	0.0535	0.0355	0.0777	0.0011	-0.0022	0.0876	0.0054	0.0842	-23.2601	-4.0543	15.7449
27	1.3511	0.3627	0.1427	0.8538	0.0309	0.1597	0.0217	0.0184	0.0546	-0.0092	-0.05	-0.0741	0.0372	-0.0016	0.0283	0.0686	0.0008	-0.0038	0.0619	0.0075	0.0945	-23.7457	12.3776	8.9949
28	0.0602	0.0757	-0.1108	0.5359	-0.2454	0.2303	0.003	-0.0046	0.0086	0.0639	-0.0051	-0.0534	-0.0106	0.0048	0.0021	0.0851	-0.0025	-0.0035	0.0659	0.0019	0.0823	-33.1944	13.3481	16.7285
29	0.922	0.7762	0.0253	0.6625	-0.0166	0.2291	0.0449	-0.0417	-0.0211	0.0599	-0.0393	-0.0251	-0.0283	0.013	-0.0056	0.0917	-0.0031	-0.0177	0.0648	0.0015	0.0948	-23.9211	15.1463	17.8724
30	0.1812	0.0632	0.0449	0.3887	-0.0251	0.0521	-0.0045	-0.0029	0.0132	0.0354	0.0018	-0.0132	-0.0037	-0.001	0.0028	0.0798	-0.0017	-0.0002	0.0644	0.0003	0.0784	-37.8042	19.8561	13.3815
31	0.2389	-0.0223	-0.0734	0.5014	0.5163	0.5735	0.0285	0.0106	0.0188	-0.0075	-0.0361	-0.0395	-0.0155	-0.0389	0.0076	0.0723	-0.0013	0.0013	0.0634	0.0034	0.0857	-36.3818	22.9366	5.3478
32	0.0837	0.1919	0.0583	0.4433	0.1379	0.0547	-0.0045	0.0073	0.0029	-0.0208	0.0141	-0.0053	0.0038	-0.0006	-0.0096	0.0769	0.0004	-0.0023	0.0704	0.0027	0.0779	-44.3569	3.2254	6.0145
33	1.5226	-0.2722	-0.4625	0.0768	-0.0119	0.4747	0.0191	0.0679	-0.02	0.0024	-0.0243	0.0132	-0.0286	0.0033	0.0052	0.0811	-0.0036	-0.0001	0.0728	-0.0031	0.0809	-60.5607	0.2226	8.0737
34	0.4217	-0.1719	-0.0889	0.2544	-0.1498	0.2103	0.0029	-0.0009	-0.001	0.0482	0.0014	0.0219	-0.0395	0.0081	-0.0043	0.0771	0.0023	0.0016	0.0668	0.0011	0.082	-49.4094	0.3477	17.3782
35	0.0491	0.0566	0.0552	0.1272	-0.0224	0.183	0.0068	-0.012	0.0074	0.0044	-0.0094	0.0097	0.006	-0.015	0.0026	0.0734	-0.0007	0.0058	0.0701	-0.0017	0.0773	-56.7598	-0.457	18.2893
36	1.453	0.4495	0.3933	0.4809	0.925	1.9954	-0.0184	-0.124	0.0618	0.0219	-0.111	0.0658	0.0529	-0.1924	0.1294	0.0515	0.0072	-0.0096	0.0665	0.0076	0.0911	-64.2778	-8.1627	21.0361
37	0.3898	0.0232	-0.0276	0.3367	-0.0554	0.0421	0.0017	0.0044	-0.0027	-0.0103	-0.0047	0.0067	-0.001	0.01	0.003	0.0751	0.0001	0.0016	0.0666	0.002	0.0819	-51.1131	-11.5481	13.8986
38	0.4067	0.3194	-0.3197	0.4253	-0.3996	0.928	-0.01	0.0468	-0.0122	-0.0151	0.0396	0.0524	0.0707	-0.0148	-0.0296	0.0682	0.0018	0.0046	0.0538	-0.0045	0.0871	-58.1785	-11.749	7.962
39	1.0725	-0.1315	0.412	0.0199	-0.0225	0.3914	-0.0074	0.0109	-0.0697	0.0059	0.0081	0.0149	0.0279	0.0241	-0.0008	0.0793	0.0037	-0.0019	0.075	0.0009	0.0786	-33.1297	-7.722	2.9627
40	11.2922	-3.0009	-0.8025	0.8041	0.1958	0.1033	0.0749	0.6402	0.7422	-0.0222	-0.1477	-0.2148	0.0616	0.1021	0.0728	0.0814	0.1955	0.0631	0.5105	0.1838	0.1241	-22.5248	-15.6748	7.8066

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	1	A	401 - 403
3	X-RAY DIFFRACTION	2	A	8 - 24
4	X-RAY DIFFRACTION	3	A	25 - 37
5	X-RAY DIFFRACTION	4	A	38 - 49
6	X-RAY DIFFRACTION	5	A	50 - 64
7	X-RAY DIFFRACTION	6	A	65 - 77
8	X-RAY DIFFRACTION	7	A	78 - 89
9	X-RAY DIFFRACTION	8	A	90 - 103
10	X-RAY DIFFRACTION	9	A	104 - 114
11	X-RAY DIFFRACTION	10	A	115 - 127
12	X-RAY DIFFRACTION	11	A	128 - 162
13	X-RAY DIFFRACTION	12	A	163 - 181
14	X-RAY DIFFRACTION	13	A	182 - 193
15	X-RAY DIFFRACTION	14	A	194 - 210
16	X-RAY DIFFRACTION	15	A	211 - 246
17	X-RAY DIFFRACTION	16	A	247 - 261
18	X-RAY DIFFRACTION	17	A	262 - 280
19	X-RAY DIFFRACTION	18	A	281 - 297
20	X-RAY DIFFRACTION	19	A	298 - 304
21	X-RAY DIFFRACTION	20	A	305 - 309
22	X-RAY DIFFRACTION	21	B	1 - 7
23	X-RAY DIFFRACTION	21	B	401 - 403
24	X-RAY DIFFRACTION	22	B	8 - 49
25	X-RAY DIFFRACTION	23	B	50 - 54
26	X-RAY DIFFRACTION	24	B	55 - 76
27	X-RAY DIFFRACTION	25	B	77 - 86
28	X-RAY DIFFRACTION	26	B	87 - 100
29	X-RAY DIFFRACTION	27	B	101 - 112
30	X-RAY DIFFRACTION	28	B	113 - 127
31	X-RAY DIFFRACTION	29	B	128 - 140
32	X-RAY DIFFRACTION	30	B	141 - 181
33	X-RAY DIFFRACTION	31	B	182 - 193
34	X-RAY DIFFRACTION	32	B	194 - 207
35	X-RAY DIFFRACTION	33	B	208 - 216
36	X-RAY DIFFRACTION	34	B	217 - 235
37	X-RAY DIFFRACTION	35	B	236 - 248
38	X-RAY DIFFRACTION	36	B	249 - 261
39	X-RAY DIFFRACTION	37	B	262 - 280
40	X-RAY DIFFRACTION	38	B	281 - 297
41	X-RAY DIFFRACTION	39	B	298 - 305
42	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