PDB-3r9b: Crystal structure of Mycobacterium smegmatis CYP164A2 in ligand f...

ID or keywords:

Entry

Database: PDB / ID: 3r9b

Title

Crystal structure of Mycobacterium smegmatis CYP164A2 in ligand free state

Components

CYTOCHROME P450 164A2

Keywords

OXIDOREDUCTASE /

Cytochrome P450 /

monooxygenase

Function / homology

Function and homology information

Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen /

monooxygenase activity / iron ion binding /

heme binding
Similarity search - Function

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.89 Å

Authors

Agnew, C.R.J. / Warrilow, A.G.S. / Kelly, S.L. / Brady, R.L.

Citation

Journal: Antimicrob.Agents Chemother. / Year: 2012
Title: An enlarged, adaptable active site in CYP164 family P450 enzymes, the sole P450 in Mycobacterium leprae.
Authors: Agnew, C.R. / Warrilow, A.G. / Burton, N.M. / Lamb, D.C. / Kelly, S.L. / Brady, R.L.

History

Deposition	Mar 25, 2011	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 4, 2012	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2024	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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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	3r9b.cif.gz	260.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3r9b.ent.gz	211.8 KB	Display	PDB format
PDBx/mmJSON format	3r9b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r9/3r9b ftp://data.pdbj.org/pub/pdb/validation_reports/r9/3r9b	HTTPS FTP

-
Related structure data

Related structure data	3r9cC C: citing same article (ref.)
Similar structure data	3cy1-d 3cxz-d 5op9-d 5edt-d 3cv9-d 2vz7-1 6rq8-d 4g2g-d 1n40-d 4ktj-d Search similar-shape structures by Omokage search (details) 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

3r9cC

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#82 - Oct 2006 Cytochrome p450 similarity (2)

Deposited unit

A: CYTOCHROME P450 164A2

B: CYTOCHROME P450 164A2

C: CYTOCHROME P450 164A2

hetero molecules

141 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CYTOCHROME P450 164A2

hetero molecules

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

2

B: CYTOCHROME P450 164A2

hetero molecules

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

3

C: CYTOCHROME P450 164A2

hetero molecules

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

Unit cell

Length a, b, c (Å)	178.396, 102.776, 92.412
Angle α, β, γ (deg.)	90.00, 90.06, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 3 / Auth seq-ID: 15 - 414 / Label seq-ID: 15 - 414

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C

-
Protein , 1 types, 3 molecules ABC

#1: Protein	CYTOCHROME P450 164A2 Mass: 45555.871 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / Gene: MSMEG_6312 / Production host: Escherichia coli (E. coli) References: UniProt: A0R5U2, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

#1: Protein

CYTOCHROME P450 164A2

Mass: 45555.871 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / Gene: MSMEG_6312 / Production host:

Escherichia coli (E. coli)
References: UniProt: A0R5U2,

Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

-
Non-polymers , 7 types, 734 molecules

#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Chemical	ChemComp-D12 / DODECANE / Dodecane Mass: 170.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₂H₂₆
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 703 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 3.1 Å³/Da / Density % sol: 60.31 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES, 0.8M Sodium dihydrogen phosphate, 0.8M Potassium dihydrogen phosphate, 3% w/v 6-Aminohexanoic acid, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9108, 1.7394, 1.7423, 1.7035

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2010

Radiation

Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9108	1
2	1.7394	1
3	1.7423	1
4	1.7035	1

Reflection

Resolution: 1.89→92.45 Å / Num. obs: 131656 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / R_merge(I) obs: 0.065

Reflection shell

Resolution: 1.9→1.96 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.676 / Mean I/σ(I) obs: 2 / % possible all: 99.7

-
Processing

Software

Name	Version	Classification
GDA		data collection
SHELXS		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 1.89→92.45 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.956 / SU B: 4.686 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20189	6616	5 %	RANDOM
R_work	0.18314	-	-	-
obs	0.18407	124989	99.52 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 16.393 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.32 Å²	0 Å²	-0.05 Å²
2-	-	0.3 Å²	0 Å²
3-	-	-	-0.62 Å²

Refinement step

Cycle: LAST / Resolution: 1.89→92.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8961	0	255	703	9919

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	9348
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.246	2.045	12742
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.992	5	1178
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.999	23	380
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.432	15	1452
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.163	15	88
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	1454
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	7056
X-RAY DIFFRACTION	r_gen_planes_other
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	0.683	1.5	5889
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.3	2	9445
X-RAY DIFFRACTION	r_scbond_it	2.01	3	3459
X-RAY DIFFRACTION	r_scangle_it	3.386	4.5	3291
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2903 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Type	Rms dev position (Å)	Weight position
A	tight positional	0.04	0.05
B	tight positional	0.02	0.05
C	tight positional	0.02	0.05
A	tight thermal	0.08	0.5
B	tight thermal	0.07	0.5
C	tight thermal	0.08	0.5

LS refinement shell

Resolution: 1.895→1.944 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.326	458	-
R_work	0.308	8826	-
obs	-	-	95.08 %

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	0.5221	-0.2918	0.8965	1.8872	-0.5834	1.6792	0.0299	0.2803	0.0672	-0.1883	-0.1715	-0.1075	0.0982	0.312	0.1416	0.2064	-0.0216	0.0579	0.3798	0.0478	0.0956	71.1014	75.3945	27.364
2	0.0124	0.0824	-0.047	1.6991	-1.004	0.5984	0.0263	0.0143	0.0204	-0.075	-0.234	-0.2801	0.023	0.1461	0.2077	0.2248	-0.0093	-0.0193	0.2418	0.1132	0.2433	67.0289	87.9083	30.6361
3	3.6167	-1.1273	-0.2098	0.8954	-0.7442	1.2782	-0.1696	-0.1742	0.2506	0.1774	0.0267	-0.1237	-0.1291	0.0822	0.1429	0.231	-0.0587	-0.056	0.155	0.0298	0.2127	63.764	87.5672	44.2966
4	6.999	-2.3108	8.0726	0.7658	-2.6624	9.3146	0.4872	-0.938	-0.46	-0.2137	0.185	0.1335	0.6975	-1.1021	-0.6722	0.3693	-0.2316	-0.0581	0.3369	0.1844	0.1982	48.0314	84.6091	32.2769
5	1.9062	-0.6775	0.1238	1.5034	-0.5018	1.0703	-0.0846	-0.1011	0.0385	0.032	0.103	0.0494	-0.012	-0.0993	-0.0184	0.1901	-0.0277	0.0055	0.1843	0.0067	0.174	52.0968	75.8617	53.5808
6	1.3411	-1.1614	-1.8812	2.8448	1.059	3.1864	-0.1632	-0.1109	-0.2652	0.146	-0.0729	-0.0472	0.2271	-0.1032	0.2361	0.1863	-0.0125	0.0584	0.287	0.184	0.3169	64.9628	53.4145	55.9387
7	4.1981	-0.2475	-1.6864	0.0441	0.0135	0.932	-0.1027	0.0281	-0.493	-0.0557	0.0548	0.074	0.2109	-0.1407	0.0479	0.2893	-0.0702	0.0268	0.1572	0.0125	0.2951	60.3122	53.2698	45.3674
8	2.0693	1.8531	-0.7366	8.5739	-1.9108	0.5594	-0.0942	0.1948	-0.1328	0.2162	0.1672	0.1638	-0.041	-0.0802	-0.073	0.234	-0.0501	-0.0115	0.2093	-0.0041	0.1439	53.6279	63.9032	36.1887
9	2.3499	1.5842	-3.6121	2.1055	-2.8346	5.9845	-0.0792	0.2863	-0.1375	-0.0715	0.0543	0.0468	0.1479	-0.3893	0.0249	0.1928	-0.0556	-0.0928	0.2136	0.0123	0.1329	46.5016	66.7054	36.2299
10	1.666	1.0634	-0.8638	2.1398	-2.1009	2.0941	-0.0566	0.1965	0.1108	-0.1153	0.0784	0.0523	0.1079	-0.0617	-0.0218	0.1828	-0.0349	0.0154	0.1819	0.0487	0.2179	40.8843	63.9008	58.5107
11	5.3323	-2.1626	-3.1388	1.0524	0.9799	2.4656	-0.1624	-0.0525	-0.2689	0.02	0.1055	0.1792	0.0837	0.0153	0.0569	0.1975	-0.0472	-0.0157	0.1853	0.0462	0.2171	47.4104	68.9041	48.6189
12	0.7895	-0.1689	0.112	0.5535	-0.1374	0.1205	-0.0993	0.0559	-0.0166	-0.0688	0.0196	-0.0467	-0.0084	0.0779	0.0797	0.198	-0.0154	0.0245	0.2118	0.0155	0.1685	72.5835	70.5978	43.5245
13	3.4233	-2.1813	0.9092	1.6857	-0.4404	0.3124	-0.1075	0.102	0.2461	-0.0451	0.0311	-0.1756	-0.0623	0.0643	0.0764	0.1845	-0.042	0.0097	0.2108	0.0619	0.2062	74.2761	80.1177	40.7186
14	1.1778	-0.6736	0.0305	0.764	0.0573	0.5958	-0.0992	-0.1176	-0.0726	0.0661	0.0206	0.0213	0.0342	0.0608	0.0785	0.1815	-0.0283	0.0424	0.18	0.0274	0.1895	71.0535	63.9777	47.6108
15	2.4216	-1.5693	0.6026	3.6575	-0.9124	0.4272	-0.1253	0.237	-0.1288	-0.0733	0.1202	0.007	0.0732	0.0389	0.005	0.2493	-0.0206	0.0454	0.2145	-0.0666	0.1449	68.0407	61.2662	34.4662
16	2.2372	0.8576	0.278	1.6274	1.2878	1.1142	-0.0964	0.2349	0.0795	-0.3687	-0.0178	0.1363	-0.3119	-0.0345	0.1142	0.2701	0.0436	-0.0699	0.256	0.0245	0.0985	64.5915	104.6303	58.1588
17	1.0035	1.4369	0.9987	2.0928	1.4617	1.0232	-0.2086	-0.0354	0.2146	-0.2764	-0.0644	0.3695	-0.1732	-0.0565	0.273	0.2359	0.0211	-0.0842	0.2175	-0.0708	0.2359	55.8047	94.8335	61.4238
18	0.7506	-0.834	0.6682	4.369	0.5779	1.1674	-0.0248	-0.1037	-0.0389	0.2834	-0.1244	0.3367	0.021	-0.1424	0.1492	0.124	-0.0056	0.0084	0.254	-0.0589	0.2084	57.7258	92.1863	75.0925
19	1.1921	-0.4199	-1.8401	3.6404	3.7769	5.6453	-0.1038	-0.0998	0.2288	0.2896	0.4506	-0.0531	0.3807	0.5587	-0.3468	0.0908	0.0518	-0.0416	0.4249	-0.0736	0.0963	68.1704	80.0492	63.0885
20	0.8991	0.5783	0.8486	2.1416	0.3694	0.8261	0.0403	-0.0029	-0.0258	0.1798	-0.0383	0.0198	0.0453	0.0096	-0.002	0.1743	0.0105	-0.0035	0.2157	-0.0033	0.1742	74.6798	89.7131	85.136
21	0.7645	0.9917	-0.0184	3.236	-3.6304	6.9166	-0.024	-0.0609	-0.0014	0.2144	-0.2731	-0.2961	-0.1853	0.4111	0.2971	0.194	0.0183	-0.1806	0.2119	-0.0107	0.3644	88.5632	112.7559	84.67
22	0.7599	-1.605	0.6299	3.5742	-1.208	0.6042	-0.0153	0.1202	0.1796	0.0904	-0.0524	-0.5021	0.0005	0.2243	0.0677	0.1243	-0.0156	-0.0231	0.3221	0.0091	0.2878	88.9618	106.4984	75.9863
23	6.972	2.1035	2.0971	1.2093	0.4832	0.6732	0.0634	0.1543	-0.1858	-0.0708	-0.0595	-0.1543	0.0437	0.058	-0.0039	0.1805	0.0257	0.021	0.2719	-0.0278	0.1483	79.1819	94.0116	64.2049
24	7.9658	-2.5234	13.1766	1.9275	-5.9376	24.7842	-0.0633	0.0669	0.1624	-0.295	-0.3336	-0.24	0.4392	0.4213	0.3969	0.1378	0.0682	0.0597	0.3013	-0.0142	0.1996	87.235	86.9746	69.1189
25	3.9712	-1.3005	2.329	2.5742	-0.0037	1.6342	0.0764	0.2131	-0.0054	-0.1916	-0.0796	0.0024	-0.0178	0.1139	0.0032	0.1482	0.0179	-0.0427	0.2161	-0.0088	0.2082	89.6391	84.1527	89.346
26	0.1746	-0.9895	0.5541	6.2747	-3.3438	1.872	0.0064	0.0592	0.0051	0.0858	-0.0483	-0.3235	-0.0498	0.042	0.0419	0.1501	0.0171	-0.0267	0.2428	-0.0369	0.2204	81.9666	87.1165	79.6396
27	0.4665	0.0566	0.0699	1.139	0.1088	0.0643	-0.0176	0.1207	0.0482	-0.0117	-0.0501	-0.0007	-0.0514	-0.0466	0.0678	0.1916	0.0167	-0.0251	0.2161	0.0081	0.172	67.9943	108.3128	74.3255
28	0.2191	0.33	-0.0607	4.4011	0.802	0.2224	0.0002	0.1068	0.0372	-0.054	-0.0519	0.2995	-0.0171	-0.068	0.0516	0.1676	0.0339	-0.0526	0.2177	-0.0178	0.2061	58.9053	105.1334	72.013
29	0.3244	0.3742	-0.0868	1.6811	0.1278	0.5939	-0.0175	-0.0671	0.0184	0.1918	-0.0719	-0.0468	-0.0515	-0.0181	0.0894	0.1599	0.0157	-0.0448	0.2005	0.0169	0.198	74.6317	109.8012	80.4941
30	1.8954	1.3242	0.6596	3.9815	0.7058	0.6165	0.0824	0.2778	0.085	-0.196	-0.0921	-0.096	-0.0777	0.0643	0.0097	0.1962	-0.0023	0.0529	0.2492	0.0783	0.148	78.5613	110.7472	64.4671
31	10.786	4.1399	-4.181	3.6123	-1.0801	1.7687	0.1136	-0.1654	0.0612	0.4761	-0.0785	0.0527	0.0253	0.1035	-0.035	0.3187	0.0274	0.0457	0.2695	0.0372	0.0116	43.1952	35.4006	98.9643
32	1.5233	-0.034	-0.6561	0.1888	0.2719	0.8423	-0.2199	-0.2673	-0.2139	0.1696	0.0188	0.0773	0.1838	0.1007	0.2011	0.283	0.0236	0.0697	0.1852	0.0655	0.1696	40.6991	30.7227	93.0642
33	2.6024	-1.9426	-0.7366	2.482	-0.3547	1.306	-0.0114	0.3043	-0.2606	-0.1195	-0.1362	0.1946	0.1299	-0.0741	0.1476	0.2129	-0.0567	0.0525	0.1616	-0.0389	0.2053	32.3123	33.3012	78.9229
34	2.0952	-1.2601	-2.1742	4.739	7.1652	10.8799	0.4622	-0.0723	-0.064	-0.6622	0.0435	-0.3332	-1.0739	0.0774	-0.5057	0.4194	-0.106	0.1295	0.1201	0.0098	0.128	27.0102	48.4181	90.9211
35	2.8779	-0.1635	-0.9056	0.6428	-0.597	0.9595	0.0806	0.2133	-0.0373	-0.0236	-0.0688	0.0455	-0.0263	-0.0379	-0.0118	0.2123	-0.0089	0.0083	0.1833	0.0037	0.1747	38.8712	49.1396	68.7496
36	1.1077	-0.1743	0.5615	2.2439	-0.3363	3.6884	-0.0363	0.0912	0.2393	-0.0091	-0.1618	-0.518	-0.2723	0.2119	0.1981	0.1154	-0.0611	-0.0326	0.1575	0.0851	0.3006	67.4444	48.4748	74.8503
37	1.4412	-1.9337	0.388	2.9414	-0.8679	0.4534	0.1027	0.0109	0.2594	0.0517	-0.1136	-0.2991	-0.1521	0.1045	0.0109	0.218	-0.0511	-0.0045	0.1756	0.0411	0.2421	56.5516	55.5471	75.8037
38	4.8526	3.9992	-2.3502	3.9881	-2.598	1.7756	0.0019	-0.0418	0.209	0.1112	-0.0061	0.0861	-0.0771	-0.0162	0.0042	0.2662	-0.0234	0.0162	0.1838	-0.0251	0.1413	44.3027	50.5883	89.811
39	0.9643	0.7577	-0.9978	7.1324	-11.4764	18.6138	-0.3307	-0.0386	0.1948	0.2058	0.1133	-0.1571	-0.394	-0.3027	0.2174	0.2963	-0.0478	0.0232	0.1202	-0.0482	0.1927	42.4051	61.8752	83.7881
40	1.8032	0.7213	-1.3803	3.8469	-2.8619	2.5564	-0.0276	-0.1575	-0.0288	0.2312	-0.0067	-0.0113	-0.1343	0.0828	0.0343	0.2265	-0.0163	0.03	0.1452	0.0266	0.2127	41.6105	64.4525	64.4657
41	2.4369	-2.157	1.8248	2.1182	-1.9401	1.8984	0.0319	0.0842	0.2759	0.0425	-0.0717	-0.1381	-0.0117	0.0596	0.0398	0.2289	-0.0273	0.05	0.1532	0.0028	0.2206	40.0435	56.8333	74.3744
42	1.0046	-0.2099	-0.1265	0.5679	0.0614	0.0704	-0.0007	-0.0375	-0.0235	0.0947	-0.0622	-0.0448	0.0825	0.0224	0.0629	0.219	-0.0025	0.003	0.1852	0.0302	0.1686	51.4177	34.1419	79.7114
43	4.0743	-1.7734	-0.822	0.9848	0.5282	0.3048	0.0131	0.0217	-0.2404	0.1066	-0.0663	0.1055	0.0746	-0.0369	0.0533	0.234	-0.0033	0.0493	0.1596	0.0371	0.2003	43.8029	28.0563	82.5357
44	1.3929	-0.5847	-0.0759	0.639	0.0304	0.5362	-0.0075	0.1279	0.1	-0.0421	-0.0812	-0.0533	0.0435	0.0454	0.0887	0.198	-0.0102	0.0038	0.1524	0.0406	0.1857	56.0951	38.8228	75.6083
45	4.7161	0.1515	-0.806	1.0602	-0.2053	0.6098	-0.101	-0.0258	0.0734	0.3198	0.0525	-0.0909	-0.0151	0.079	0.0485	0.234	-0.0204	-0.0769	0.2108	-0.0039	0.1499	57.2327	42.7394	88.7706

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	15 - 38
2	X-RAY DIFFRACTION	2	A	39 - 55
3	X-RAY DIFFRACTION	3	A	56 - 72
4	X-RAY DIFFRACTION	4	A	73 - 84
5	X-RAY DIFFRACTION	5	A	94 - 120
6	X-RAY DIFFRACTION	6	A	121 - 138
7	X-RAY DIFFRACTION	7	A	139 - 171
8	X-RAY DIFFRACTION	8	A	172 - 186
9	X-RAY DIFFRACTION	9	A	187 - 219
10	X-RAY DIFFRACTION	10	A	220 - 238
11	X-RAY DIFFRACTION	11	A	239 - 259
12	X-RAY DIFFRACTION	12	A	260 - 319
13	X-RAY DIFFRACTION	13	A	320 - 353
14	X-RAY DIFFRACTION	14	A	354 - 397
15	X-RAY DIFFRACTION	15	A	398 - 414
16	X-RAY DIFFRACTION	16	B	15 - 38
17	X-RAY DIFFRACTION	17	B	39 - 55
18	X-RAY DIFFRACTION	18	B	56 - 72
19	X-RAY DIFFRACTION	19	B	73 - 84
20	X-RAY DIFFRACTION	20	B	94 - 124
21	X-RAY DIFFRACTION	21	B	125 - 138
22	X-RAY DIFFRACTION	22	B	139 - 171
23	X-RAY DIFFRACTION	23	B	172 - 192
24	X-RAY DIFFRACTION	24	B	193 - 219
25	X-RAY DIFFRACTION	25	B	220 - 238
26	X-RAY DIFFRACTION	26	B	239 - 259
27	X-RAY DIFFRACTION	27	B	260 - 319
28	X-RAY DIFFRACTION	28	B	320 - 354
29	X-RAY DIFFRACTION	29	B	355 - 392
30	X-RAY DIFFRACTION	30	B	393 - 414
31	X-RAY DIFFRACTION	31	C	15 - 25
32	X-RAY DIFFRACTION	32	C	26 - 55
33	X-RAY DIFFRACTION	33	C	56 - 72
34	X-RAY DIFFRACTION	34	C	73 - 84
35	X-RAY DIFFRACTION	35	C	94 - 124
36	X-RAY DIFFRACTION	36	C	125 - 147
37	X-RAY DIFFRACTION	37	C	148 - 171
38	X-RAY DIFFRACTION	38	C	172 - 192
39	X-RAY DIFFRACTION	39	C	193 - 220
40	X-RAY DIFFRACTION	40	C	221 - 238
41	X-RAY DIFFRACTION	41	C	239 - 259
42	X-RAY DIFFRACTION	42	C	260 - 319
43	X-RAY DIFFRACTION	43	C	320 - 353
44	X-RAY DIFFRACTION	44	C	354 - 397
45	X-RAY DIFFRACTION	45	C	398 - 414

-
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

-
Protein , 1 types, 3 molecules ABC

-
Non-polymers , 7 types, 734 molecules

-
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

-Protein , 1 types, 3 molecules ABC

-Non-polymers , 7 types, 734 molecules

-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

-
Protein , 1 types, 3 molecules ABC

-
Non-polymers , 7 types, 734 molecules

-
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