PDB-4bwt: Three-dimensional structure of Paracoccus pantotrophus pseudoazur...

ID or keywords:

Entry

Database: PDB / ID: 4bwt

Title

Three-dimensional structure of Paracoccus pantotrophus pseudoazurin at pH 6.5

Components

PSEUDOAZURIN

Keywords

ELECTRON TRANSPORT

Function / homology

Function and homology information

periplasmic space /

electron transfer activity / copper ion binding
Similarity search - Function

Biological species

PARACOCCUS PANTOTROPHUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.76 Å

Authors

Freire, F. / Mestre, A. / Pinho, J. / Najmudin, S. / Bonifacio, C. / Pauleta, S.R. / Romao, M.J.

Citation

Journal: To be Published
Title: Exploring the Surface Determinants of Paracoccus Pantotrophus Pseudoazurin
Authors: Freire, F. / Mestre, A. / Pinho, J. / Najmudin, S. / Bonifacio, C. / Pauleta, S.R. / Romao, M.J.

History

Deposition	Jul 4, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 16, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_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_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_conn.ptnr2_label_seq_id / _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	4bwt.cif.gz	120.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4bwt.ent.gz	95.5 KB	Display	PDB format
PDBx/mmJSON format	4bwt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	4bwuC 4bxvC 3erxS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4zlt-1 6gvd-d 4lq5-1 1j1n-2 3vlu-d 5h71-1 3i54-1 1y3n-d 6gwf-d 4zgz-1 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: PSEUDOAZURIN

B: PSEUDOAZURIN

hetero molecules

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

1

A: PSEUDOAZURIN

B: PSEUDOAZURIN

hetero molecules

A: PSEUDOAZURIN

B: PSEUDOAZURIN

hetero molecules

defined by author&software
54.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	107.280, 57.870, 67.100
Angle α, β, γ (deg.)	90.00, 125.99, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	PSEUDOAZURIN Mass: 13358.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PARACOCCUS PANTOTROPHUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P80401
#2: Chemical	ChemComp-CU / COPPER (II) ION / Copper Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 3.16 Å³/Da / Density % sol: 62 % / Description: NONE
Crystal grow	pH: 6.5 Details: 3.0 - 3.2 M AMMONIUM SULPHATE, 50 MM POTASSIUM PHOSPHATE PH 6.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
Detector	Type: ADSC QUANTUM 4 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 1.76→27.85 Å / Num. obs: 32561 / % possible obs: 98.5 % / Observed criterion σ(I): 11.8 / Redundancy: 3.4 % / R_merge(I) obs: 0.06 / Net I/σ(I): 11.8
Reflection shell	Resolution: 1.76→1.8 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.16 / Mean I/σ(I) obs: 5.1 / % possible all: 97.4

-
Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ERX

3erx

Resolution: 1.76→27.85 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.917 / SU B: 3.551 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20631	1653	5.1 %	RANDOM
R_work	0.1659	-	-	-
obs	0.16801	30907	98.33 %	-

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: 14.227 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.01 Å²	0 Å²	-0.34 Å²
2-	-	0.43 Å²	0 Å²
3-	-	-	-0.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.76→27.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1865	0	22	438	2325

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.019	1985
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1929
X-RAY DIFFRACTION	r_angle_refined_deg	2.155	1.989	2694
X-RAY DIFFRACTION	r_angle_other_deg	0.927	3	4494
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.761	5	264
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.543	25.75	80
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.31	15	366
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	6.599	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.119	0.2	302
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	2227
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	391
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.72	0.583	1005
X-RAY DIFFRACTION	r_mcbond_other	0.717	0.582	1004
X-RAY DIFFRACTION	r_mcangle_it	1.146	0.87	1259
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.853	0.785	980
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.76→1.806 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.24	116	-
R_work	0.208	2258	-
obs	-	-	97.14 %

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	0.3128	-0.7655	0.5175	3.9685	-0.8542	0.9398	-0.0252	-0.0163	0.0171	-0.0384	-0.031	0.0458	-0.0686	-0.0394	0.0562	0.0378	-0.0124	-0.0122	0.0347	-0.0028	0.0442	-1.3374	33.3237	10.7359
2	1.4986	1.1618	-1.268	2.4092	-1.0573	1.1277	-0.049	0.0962	-0.046	-0.0276	0.0652	-0.0427	0.0795	-0.0507	-0.0161	0.0502	0.0149	-0.0296	0.045	-0.0222	0.0795	5.2286	19.9865	7.9029
3	1.2494	-0.5203	0.5333	0.4655	0.0895	0.6801	0.035	0.0294	-0.0437	-0.0178	-0.0176	-0.0029	-0.0309	-0.0108	-0.0175	0.0362	0.0019	-0.0068	0.0402	-0.0002	0.0391	5.6087	24.1447	12.3263
4	1.1076	-0.5803	0.8054	0.6355	-0.8074	1.1441	0.0842	-0.1071	0.0386	-0.1843	-0.0913	-0.0119	0.0694	0.1395	0.0071	0.2836	-0.0195	0.0091	0.0957	-0.0099	0.0116	6.2699	39.9773	14.5529
5	2.7747	4.2069	1.6196	8.6497	2.4355	1.6621	-0.0539	-0.1447	0.1195	-0.0943	-0.0536	0.1279	-0.0765	-0.0764	0.1075	0.0555	0.0018	-0.014	0.0232	-0.0152	0.0238	-2.6871	39.8981	15.7794
6	1.3771	-0.5893	1.4084	3.2004	1.2014	2.5457	0.0156	0.0123	-0.0605	-0.0852	-0.0418	0.179	-0.0356	-0.0112	0.0262	0.027	-0.0205	0.0006	0.0373	0.0072	0.0452	-4.8742	23.5984	11.4887
7	0.7851	1.0304	1.0133	2.5291	3.573	5.585	-0.0014	-0.022	0.0192	0.0003	-0.0306	0.0329	-0.0016	-0.028	0.032	0.0368	-0.0132	-0.0077	0.0502	0.0099	0.0329	-2.0154	23.8385	20.2172
8	5.3872	-1.4653	1.5467	3.5848	0.0315	3.8794	-0.0042	-0.0741	-0.294	0.4193	-0.0355	-0.1027	0.0725	0.0469	0.0397	0.0688	-0.011	-0.0191	0.0428	0.0128	0.0346	5.3823	30.329	28.9504
9	9.8307	5.1278	2.2623	8.0996	1.6475	0.5638	-0.0454	-0.1563	0.3339	0.1463	-0.0586	0.2823	0.0188	-0.0336	0.104	0.1083	-0.0049	0.0458	0.0329	-0.0084	0.0326	1.0124	38.2739	29.4603
10	2.7805	2.383	3.41	2.0598	2.9278	4.184	0.1273	-0.1862	-0.0101	0.0906	-0.1189	-0.0015	0.1445	-0.2184	-0.0084	0.0258	-0.0347	0.0063	0.0908	0.0179	0.0374	-7.0664	24.7055	22.2865
11	4.9597	5.0531	2.6851	6.9875	2.049	1.7855	0.0481	-0.0545	0.0362	0.2081	-0.0419	-0.004	-0.0231	-0.1101	-0.0062	0.0342	-0.007	-0.0049	0.0879	0.0187	0.0418	-5.2366	34.9826	18.8207
12	0.4671	-0.4863	-0.397	2.6396	2.77	2.941	0.021	0.0514	-0.042	-0.1733	-0.0662	0.0535	-0.1849	-0.0552	0.0452	0.0764	-0.0068	-0.0008	0.0404	-0.0033	0.0052	3.6535	40.4661	23.7165
13	0.8907	-0.0777	0.0336	0.8466	0.4157	0.2114	-0.0188	-0.1206	-0.0705	0.0163	0.0025	0.0692	0.0109	-0.0049	0.0163	0.0401	-0.0084	-0.0165	0.0576	0.0068	0.0586	1.697	22.2629	21.9904
14	0.5249	-0.4164	0.5873	0.3983	-0.6206	1.0106	0.1406	-0.1524	-0.0868	-0.0863	0.0431	0.1092	0.0964	0.014	-0.1837	0.0745	-0.0578	-0.009	0.1543	-0.0059	0.0665	6.3053	19.5833	20.6593
15	0.0654	0.649	-0.0323	6.6667	-0.9164	1.7064	-0.0128	0.0035	-0.0049	-0.081	0.024	-0.0293	-0.0642	0.0703	-0.0112	0.0394	-0.0131	0.0013	0.0413	0.0038	0.0384	6.8174	35.044	19.1185
16	2.7578	0.9903	0.7079	1.0256	2.1487	5.5421	0.0117	-0.0441	0.0778	-0.2375	0.0389	-0.0087	-0.6643	0.0598	-0.0505	0.1311	-0.019	0.0177	0.0716	-0.0442	0.0287	10.8307	43.5418	23.842
17	1.7013	-2.1896	-0.9352	11.8863	-3.2349	2.6893	0.0532	-0.1826	0.1606	0.1804	-0.0155	-0.3322	-0.1466	0.2239	-0.0377	0.0307	-0.0052	-0.0214	0.0489	-0.0248	0.047	15.6112	35.109	27.0601
18	0.205	0.5455	-0.5306	3.9302	-0.7227	1.5687	-0.0138	-0.0561	-0.0037	0.1007	0.0302	-0.0873	0.0653	0.188	-0.0164	0.0426	0.0119	-0.0165	0.0509	0.0126	0.0223	13.2227	22.5698	25.3333
19	0.3967	0.5604	0.0368	4.5186	2.0348	2.1148	-0.0979	0.0622	-0.0635	-0.022	0.0263	0.0495	0.0213	0.145	0.0716	0.0419	-0.0041	0.0281	0.0636	0.002	0.0273	13.9673	25.809	18.5896
20	3.4911	-0.1059	-1.0352	2.3109	-0.8275	0.6267	0.0986	-0.0252	0.1107	0.0283	-0.0954	-0.0733	-0.0401	0.0438	-0.0033	0.0467	-0.0254	-0.0017	0.0328	0.004	0.0276	14.4039	35.6776	16.7102
21	1.334	-0.3725	0.5438	11.1877	1.0973	0.3625	-0.0105	-0.0214	-0.0626	-0.0347	0.0245	0.1121	-0.0084	-0.0082	-0.014	0.0361	-0.0081	0.0071	0.0316	-0.0019	0.0213	8.9298	27.1359	-2.6798
22	1.981	-0.1439	-3.3482	3.0179	-2.4533	8.0788	-0.0415	0.0895	0.0676	0.1258	0.1677	0.025	-0.0309	-0.3026	-0.1262	0.0417	0.0025	-0.0063	0.0193	0.0073	0.0529	7.6104	40.4799	4.3007
23	0.303	-0.1669	-0.054	3.201	1.4947	0.7002	-0.0664	0.0403	0.1045	0.0548	0.0343	0.0424	0.0204	0.0144	0.0322	0.049	-0.0004	-0.0076	0.0522	0.0071	0.0502	12.0546	38.3904	3.0256
24	3.6253	-2.5601	-0.797	4.6638	-0.6101	0.6569	0.0525	-0.0958	-0.0284	-0.2358	-0.088	-0.0564	0.0686	0.0836	0.0354	0.027	-0.0017	-0.0045	0.0356	0.0068	0.045	14.01	24.8227	4.8241
25	6.4684	-1.6403	3.231	0.6172	-0.9746	2.6395	0.0653	0.1047	-0.2566	-0.0033	-0.0662	0.0973	0.0375	-0.0347	0.0009	0.043	-0.0012	-0.0052	0.0322	-0.016	0.0717	14.8106	17.1149	-2.8326
26	0.9972	-2.0056	0.2594	9.4028	1.309	2.4309	-0.0525	-0.0724	-0.0657	-0.15	0.1186	-0.0104	-0.0914	0.0047	-0.066	0.0355	-0.0113	-0.0025	0.0294	0.0067	0.0243	10.8085	29.5474	-5.9322
27	5.2449	-2.2432	-0.2798	2.4241	1.9213	2.2318	-0.0049	-0.0916	0.125	-0.0887	0.0142	-0.0513	-0.1036	-0.018	-0.0093	0.0525	0.0104	-0.0159	0.0182	0.0147	0.0356	9.7639	41.4312	-6.2312
28	4.5845	-2.5875	0.452	2.4103	-1.0463	0.7546	0.0495	-0.0837	0.0775	-0.1059	-0.0376	-0.0632	-0.0052	0.0593	-0.0119	0.1167	0.003	0.0355	0.0327	-0.0058	0.0475	23.9995	32.8779	-5.0705
29	1.9923	-2.7666	0.4111	5.8625	-0.0761	0.2064	0.0784	0.081	0.1144	-0.1176	-0.1038	-0.1784	0.0134	0.0212	0.0254	0.0088	0.006	0.015	0.0451	0.0199	0.0657	28.2872	25.2004	-2.3922
30	2.5967	-5.4142	0.9036	12.9022	-4.1885	3.6074	0.1434	0.0854	0.0688	-0.2706	-0.195	-0.1679	0.0066	0.0494	0.0516	0.0094	-0.0003	0.0055	0.0375	0.0001	0.038	23.9764	29.034	-9.8794
31	10.1453	-1.9063	-0.7038	0.368	0.2363	3.1716	0.0647	0.3554	0.2344	-0.0301	-0.0567	-0.0342	0.1083	0.0713	-0.008	0.0821	-0.0082	-0.0286	0.0473	0.0243	0.021	13.9545	38.0141	-13.2515
32	0.3399	-1.1533	0.6972	4.1943	-1.6018	3.5327	0.0193	0.0417	-0.0033	-0.0535	-0.0682	0.0261	0.0175	0.2475	0.0489	0.0186	0.0114	0.0007	0.0549	-0.0047	0.0474	15.2242	25.3289	-8.8413
33	0.3886	-0.7287	0.038	1.4453	-0.2871	0.6317	-0.0091	-0.0007	-0.0293	0.035	-0.02	0.0334	-0.0439	0.0915	0.0292	0.017	0.0021	0.0004	0.0436	-0.0035	0.0495	22.0739	26.7779	-2.4858
34	1.1284	0.3541	0.6196	3.873	-0.2691	0.3975	-0.0124	0.1602	0.1952	-0.0687	-0.0841	0.1396	-0.0006	0.1068	0.0966	0.0498	-0.0151	-0.0145	0.0544	0.0105	0.0526	19.8411	43.0108	-0.9482
35	0.4941	-0.6274	-0.217	5.9878	-0.1164	0.125	0.005	-0.0642	-0.0146	0.0391	-0.0138	-0.0295	-0.0069	0.036	0.0088	0.0357	-0.0031	-0.0108	0.0406	0.0004	0.0479	18.6515	30.4924	2.7385
36	9.5301	0.213	0.3071	0.2724	-1.0278	4.231	-0.0456	-0.0852	-0.2338	-0.0065	0.0348	0.0017	0.1587	-0.0019	0.0108	0.09	0.0714	0.0173	0.0609	0.0144	0.0688	23.4837	17.1929	4.3911
37	0.7286	-0.0728	0.5239	5.7974	0.7398	4.0135	-0.0427	-0.0162	0.0057	0.1495	0.1851	-0.1872	0.0826	0.1745	-0.1425	0.0111	0.0176	-0.0131	0.0508	-0.0062	0.0524	29.0503	25.3609	7.3693
38	0.3871	-1.1033	-0.0431	3.5796	-0.7327	1.713	0.0206	0.0378	0.0239	0.0664	-0.1497	-0.1486	-0.2106	0.0835	0.1291	0.0436	-0.0314	-0.0105	0.0381	-0.0066	0.0754	27.273	38.8808	6.1331
39	1.675	-1.4232	0.5463	2.132	-1.5891	3.2198	-0.0668	-0.0948	-0.0228	0.18	0.0287	0.0314	-0.101	0.1007	0.0381	0.0316	-0.0104	0.0047	0.0265	-0.0065	0.0363	22.3479	35.7877	8.7353
40	0.1303	0.082	-0.5925	2.7835	0.9204	3.3825	-0.0217	-0.0029	-0.0148	0.0717	0.0116	-0.0692	0.0801	-0.0089	0.0101	0.0392	0.013	0.0065	0.0252	0.02	0.0501	19.4018	26.8449	10.4735

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 - 13
3	X-RAY DIFFRACTION	3	A	14 - 21
4	X-RAY DIFFRACTION	4	A	22 - 26
5	X-RAY DIFFRACTION	5	A	27 - 32
6	X-RAY DIFFRACTION	6	A	33 - 38
7	X-RAY DIFFRACTION	7	A	39 - 44
8	X-RAY DIFFRACTION	8	A	45 - 48
9	X-RAY DIFFRACTION	9	A	49 - 54
10	X-RAY DIFFRACTION	10	A	55 - 62
11	X-RAY DIFFRACTION	11	A	63 - 68
12	X-RAY DIFFRACTION	12	A	69 - 75
13	X-RAY DIFFRACTION	13	A	76 - 81
14	X-RAY DIFFRACTION	14	A	82 - 86
15	X-RAY DIFFRACTION	15	A	87 - 92
16	X-RAY DIFFRACTION	16	A	93 - 98
17	X-RAY DIFFRACTION	17	A	99 - 104
18	X-RAY DIFFRACTION	18	A	105 - 112
19	X-RAY DIFFRACTION	19	A	113 - 117
20	X-RAY DIFFRACTION	20	A	118 - 123
21	X-RAY DIFFRACTION	21	B	1 - 7
22	X-RAY DIFFRACTION	22	B	8 - 13
23	X-RAY DIFFRACTION	23	B	14 - 19
24	X-RAY DIFFRACTION	24	B	20 - 24
25	X-RAY DIFFRACTION	25	B	25 - 30
26	X-RAY DIFFRACTION	26	B	31 - 35
27	X-RAY DIFFRACTION	27	B	36 - 41
28	X-RAY DIFFRACTION	28	B	42 - 46
29	X-RAY DIFFRACTION	29	B	47 - 52
30	X-RAY DIFFRACTION	30	B	53 - 57
31	X-RAY DIFFRACTION	31	B	58 - 62
32	X-RAY DIFFRACTION	32	B	63 - 68
33	X-RAY DIFFRACTION	33	B	69 - 79
34	X-RAY DIFFRACTION	34	B	80 - 84
35	X-RAY DIFFRACTION	35	B	85 - 91
36	X-RAY DIFFRACTION	36	B	92 - 97
37	X-RAY DIFFRACTION	37	B	98 - 103
38	X-RAY DIFFRACTION	38	B	104 - 111
39	X-RAY DIFFRACTION	39	B	112 - 116
40	X-RAY DIFFRACTION	40	B	117 - 123

-
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