PDB-4c65: Crystal structure of A. niger ochratoxinase

ID or keywords:

Entry

Database: PDB / ID: 4c65

Title

Crystal structure of A. niger ochratoxinase

Components

OCHRATOXINASE

Keywords

HYDROLASE / METAL-DEPENDENT AMIDOHYDROLASE / OCHRATOXIN A HYDROLYSIS / AMIDOHYDROLASE SUPERFAMILY

Function / homology

Function and homology information

ochratoxin A catabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / carboxypeptidase activity / metallopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function

Biological species

ASPERGILLUS NIGER (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Dobritzsch, D. / Wang, H. / Schneider, G. / Yu, S.

Citation

Journal: Biochem.J. / Year: 2014
Title: Structural and Functional Characterization of Ochratoxinase, a Novel Mycotoxin Degrading Enzyme.
Authors: Dobritzsch, D. / Wang, H. / Schneider, G. / Yu, S.

History

Deposition	Sep 17, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 2, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 3, 2014	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / 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 / struct_ncs_dom_lim 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 / _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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4c65.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb4c65.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	4c65.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4c65_validation.pdf.gz	488.8 KB	Display	wwPDB validaton report
Full document	4c65_full_validation.pdf.gz	528.3 KB	Display
Data in XML	4c65_validation.xml.gz	126.4 KB	Display
Data in CIF	4c65_validation.cif.gz	176.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c6/4c65 ftp://data.pdbj.org/pub/pdb/validation_reports/c6/4c65	HTTPS FTP

-
Related structure data

Related structure data	4c5yC 4c5zC 4c60SC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4c60-2 4c60-1 4c5z-1 4c5y-1 3dug-d 3be7-d 3mtw-2 2qs8-3 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
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (4) #158 - Feb 2013 Proton-Gated Urea Channel similarity (4)

Deposited unit

A: OCHRATOXINASE

B: OCHRATOXINASE

C: OCHRATOXINASE

D: OCHRATOXINASE

E: OCHRATOXINASE

F: OCHRATOXINASE

G: OCHRATOXINASE

H: OCHRATOXINASE

373 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: OCHRATOXINASE

B: OCHRATOXINASE

C: OCHRATOXINASE

D: OCHRATOXINASE

A: OCHRATOXINASE

B: OCHRATOXINASE

C: OCHRATOXINASE

D: OCHRATOXINASE

defined by author&software
373 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: OCHRATOXINASE

F: OCHRATOXINASE

G: OCHRATOXINASE

H: OCHRATOXINASE

E: OCHRATOXINASE

F: OCHRATOXINASE

G: OCHRATOXINASE

H: OCHRATOXINASE

defined by author&software
373 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	210.855, 78.920, 217.000
Angle α, β, γ (deg.)	90.00, 105.05, 90.00
Int Tables number	5
Space group name H-M	I121

Components on special symmetry positions

ID	Model	Components
1	1	A-2051- HOH
2	1	E-2042- HOH
3	1	E-2044- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	ALA	LEU	LEU	A	A	47 - 480	5 - 438
2	1	ALA	ALA	LEU	LEU	B	B	47 - 480	5 - 438
1	2	GLU	GLU	LEU	LEU	A	A	46 - 480	4 - 438
2	2	GLU	GLU	LEU	LEU	C	C	46 - 480	4 - 438
1	3	GLU	GLU	PHE	PHE	A	A	46 - 479	4 - 437
2	3	GLU	GLU	PHE	PHE	D	D	46 - 479	4 - 437
1	4	GLU	GLU	PHE	PHE	A	A	46 - 479	4 - 437
2	4	GLU	GLU	PHE	PHE	E	E	46 - 479	4 - 437
1	5	ALA	ALA	PHE	PHE	A	A	47 - 479	5 - 437
2	5	ALA	ALA	PHE	PHE	F	F	47 - 479	5 - 437
1	6	GLU	GLU	LEU	LEU	A	A	46 - 480	4 - 438
2	6	GLU	GLU	LEU	LEU	G	G	46 - 480	4 - 438
1	7	ALA	ALA	LEU	LEU	A	A	47 - 480	5 - 438
2	7	ALA	ALA	LEU	LEU	H	H	47 - 480	5 - 438
1	8	ALA	ALA	LEU	LEU	B	B	47 - 480	5 - 438
2	8	ALA	ALA	LEU	LEU	C	C	47 - 480	5 - 438
1	9	ALA	ALA	LEU	LEU	B	B	47 - 480	5 - 438
2	9	ALA	ALA	LEU	LEU	D	D	47 - 480	5 - 438
1	10	ALA	ALA	LEU	LEU	B	B	47 - 480	5 - 438
2	10	ALA	ALA	LEU	LEU	E	E	47 - 480	5 - 438
1	11	ALA	ALA	LEU	LEU	B	B	47 - 480	5 - 438
2	11	ALA	ALA	LEU	LEU	F	F	47 - 480	5 - 438
1	12	ALA	ALA	PHE	PHE	B	B	47 - 479	5 - 437
2	12	ALA	ALA	PHE	PHE	G	G	47 - 479	5 - 437
1	13	ALA	ALA	LEU	LEU	B	B	47 - 480	5 - 438
2	13	ALA	ALA	LEU	LEU	H	H	47 - 480	5 - 438
1	14	GLU	GLU	LEU	LEU	C	C	46 - 480	4 - 438
2	14	GLU	GLU	LEU	LEU	D	D	46 - 480	4 - 438
1	15	GLU	GLU	LEU	LEU	C	C	46 - 480	4 - 438
2	15	GLU	GLU	LEU	LEU	E	E	46 - 480	4 - 438
1	16	ALA	ALA	LEU	LEU	C	C	47 - 480	5 - 438
2	16	ALA	ALA	LEU	LEU	F	F	47 - 480	5 - 438
1	17	GLU	GLU	LEU	LEU	C	C	46 - 480	4 - 438
2	17	GLU	GLU	LEU	LEU	G	G	46 - 480	4 - 438
1	18	ALA	ALA	LEU	LEU	C	C	47 - 480	5 - 438
2	18	ALA	ALA	LEU	LEU	H	H	47 - 480	5 - 438
1	19	GLU	GLU	LEU	LEU	D	D	46 - 480	4 - 438
2	19	GLU	GLU	LEU	LEU	E	E	46 - 480	4 - 438
1	20	ALA	ALA	PHE	PHE	D	D	47 - 479	5 - 437
2	20	ALA	ALA	PHE	PHE	F	F	47 - 479	5 - 437
1	21	GLU	GLU	LEU	LEU	D	D	46 - 480	4 - 438
2	21	GLU	GLU	LEU	LEU	G	G	46 - 480	4 - 438
1	22	ALA	ALA	LEU	LEU	D	D	47 - 480	5 - 438
2	22	ALA	ALA	LEU	LEU	H	H	47 - 480	5 - 438
1	23	ALA	ALA	PHE	PHE	E	E	47 - 479	5 - 437
2	23	ALA	ALA	PHE	PHE	F	F	47 - 479	5 - 437
1	24	GLU	GLU	LEU	LEU	E	E	46 - 480	4 - 438
2	24	GLU	GLU	LEU	LEU	G	G	46 - 480	4 - 438
1	25	ALA	ALA	LEU	LEU	E	E	47 - 480	5 - 438
2	25	ALA	ALA	LEU	LEU	H	H	47 - 480	5 - 438
1	26	ALA	ALA	LEU	LEU	F	F	47 - 480	5 - 438
2	26	ALA	ALA	LEU	LEU	G	G	47 - 480	5 - 438
1	27	ALA	ALA	LEU	LEU	F	F	47 - 480	5 - 438
2	27	ALA	ALA	LEU	LEU	H	H	47 - 480	5 - 438
1	28	ALA	ALA	LEU	LEU	G	G	47 - 480	5 - 438
2	28	ALA	ALA	LEU	LEU	H	H	47 - 480	5 - 438

NCS ensembles :
NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.4106, -0.001661, 0.9118), (-0.000724, -1, -0.002147), (0.9118, -0.001542, 0.4106)	-0.0863, 4.467, 0.0413
2	given	(0.0011, 0.00405, -1), (0.001057, 1, 0.004051), (1, -0.001061, 0.001095)	-0.1144, 0.05347, 0.05626
3	given	(-0.9162, -0.002914, -0.4007), (0.005075, -1, -0.004332), (-0.4007, -0.006003, 0.9162)	-0.00372, 4.534, 0.2477
4	given	(-1, 0.004862, -0.002415), (0.004852, 1, 0.004321), (0.002436, 0.004309, -1)	27.89, 13.89, -104.6
5	given	(0.4253, -0.005007, -0.905), (-0.006069, -1, 0.00268), (-0.905, 0.004353, -0.4253)	28.35, 18.22, -104.9
6	given	(0.0174, 0.000684, 0.9998), (0.000762, 1, -0.000698), (-0.9998, 0.000774, 0.0174)	28.3, 13.79, -104.7
7	given	(0.9057, -0.00541, 0.424), (-0.005932, -1, -8.8E-5), (0.424, -0.002435, -0.9057)	28.31, 18.25, -104.7

#1: Protein	OCHRATOXINASE / PROLIDASE Mass: 46646.828 Da / Num. of mol.: 8 Fragment: EXTRACELLULAR, N-TERMINALLY TRUNCATED ISOFORM, RESIDUES 43-480 Source method: isolated from a genetically manipulated source Details: 42 RESIDUES TRUNCATED AT N-TERMINUS / Source: (gene. exp.) ASPERGILLUS NIGER (mold) / Strain: UVK143 / Plasmid: PGAPT-OTASE / Production host: ASPERGILLUS NIGER (mold) / Strain (production host): AP4 References: UniProt: A2R2V4, Xaa-Pro dipeptidase, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1237 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE CRYSTALLIZED EXTRACELLULAR ISOFORM IS N-TERMINALLY TRUNCATED BY 42 AMINO ACIDS

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.8 % / Description: NONE
Crystal grow	pH: 5 Details: 16% (W/V) PEG 3000, 0.1 M CITRATE PH 5.0, 0.2 M TRI-POTASSIUM CITRATE, 3 MM N-(4- METHOXYPHENYLAZOFORMYL)-PHENYLALANINE, 0.1 MM ZNCL2

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
Detector	Type: ADSC CCD / Detector: CCD / Date: Sep 29, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9334 Å / Relative weight: 1
Reflection	Resolution: 2.2→37.8 Å / Num. obs: 153345 / % possible obs: 87.7 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / B_iso Wilson estimate: 20.5 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 6.1
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 73.4

-
Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
iMOSFLM		data reduction
SCALA		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C60

4c60

Resolution: 2.2→37.79 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.923 / SU B: 14.551 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.431 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE NOT MODELED RESIDUES A43-44, B43-46, B341-344, C43-45, D43-45, E43-45, F43-46, G43-45, G341-344, H43-46, H341-345 ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24507	7696	5 %	RANDOM
R_work	0.21295	-	-	-
obs	0.21454	145645	87.59 %	-

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: 27.585 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.09 Å²	0 Å²	-0.97 Å²
2-	-	0.69 Å²	0 Å²
3-	-	-	-0.3 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→37.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25974	0	0	1237	27211

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	26647
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	25529
X-RAY DIFFRACTION	r_angle_refined_deg	1.431	1.964	36193
X-RAY DIFFRACTION	r_angle_other_deg	1.546	3	58823
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.998	5	3481
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.672	24.066	1092
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.566	15	4276
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.241	15	156
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	3969
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	30626
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	5834
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	0.558	1.118	13870
X-RAY DIFFRACTION	r_mcbond_other	0.558	1.118	13869
X-RAY DIFFRACTION	r_mcangle_it	0.992	1.675	17324
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.58	1.189	12777
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

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	26266	0.08
1	2	B	26266	0.08
2	1	A	26422	0.08
2	2	C	26422	0.08
3	1	A	26258	0.09
3	2	D	26258	0.09
4	1	A	26378	0.09
4	2	E	26378	0.09
5	1	A	26435	0.08
5	2	F	26435	0.08
6	1	A	26126	0.09
6	2	G	26126	0.09
7	1	A	26050	0.09
7	2	H	26050	0.09
8	1	B	26050	0.09
8	2	C	26050	0.09
9	1	B	26111	0.08
9	2	D	26111	0.08
10	1	B	26121	0.09
10	2	E	26121	0.09
11	1	B	26221	0.09
11	2	F	26221	0.09
12	1	B	25766	0.09
12	2	G	25766	0.09
13	1	B	26005	0.09
13	2	H	26005	0.09
14	1	C	26311	0.08
14	2	D	26311	0.08
15	1	C	26238	0.09
15	2	E	26238	0.09
16	1	C	26262	0.09
16	2	F	26262	0.09
17	1	C	26143	0.09
17	2	G	26143	0.09
18	1	C	26195	0.09
18	2	H	26195	0.09
19	1	D	26232	0.09
19	2	E	26232	0.09
20	1	D	26172	0.09
20	2	F	26172	0.09
21	1	D	26243	0.08
21	2	G	26243	0.08
22	1	D	26072	0.08
22	2	H	26072	0.08
23	1	E	26230	0.08
23	2	F	26230	0.08
24	1	E	25995	0.09
24	2	G	25995	0.09
25	1	E	25888	0.09
25	2	H	25888	0.09
26	1	F	25913	0.09
26	2	G	25913	0.09
27	1	F	26016	0.09
27	2	H	26016	0.09
28	1	G	25896	0.09
28	2	H	25896	0.09

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.361	450	-
R_work	0.325	8979	-
obs	-	-	73.27 %

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	1.0121	-0.1639	0.5835	2.2521	-1.2723	3.1847	0.01	0.2472	0.0184	-0.2634	0.0419	-0.0266	-0.0774	-0.0125	-0.0519	0.095	-0.0026	-0.0248	0.1213	-0.0008	0.0363	-23.0366	22.8092	-43.9283
2	0.691	-0.0928	0.4645	0.5347	-0.0452	0.3312	0.0444	0.0177	0.0043	0.0986	-0.0227	-0.0001	0.054	-0.0164	-0.0218	0.1157	-0.007	-0.0337	0.0485	0.0235	0.024	-14.224	13.3886	-17.5011
3	2.9964	-4.3179	-0.9581	6.2264	1.5542	7.331	-0.2517	-0.112	-0.7785	0.34	0.1054	1.1202	0.6374	-1.2102	0.1464	0.2902	-0.0005	0.0027	0.2618	0.0228	0.2141	-25.0907	23.5209	-3.7642
4	1.0253	-0.1984	0.4482	1.4495	0.294	1.7295	-0.0417	-0.0531	0.0445	0.0593	0.0093	0.1613	-0.1372	-0.4054	0.0324	0.1015	0.0347	-0.0141	0.1157	0.0191	0.0417	-26.5115	25.4635	-25.04
5	2.1607	0.9394	0.9306	1.9812	0.4374	1.7804	0.0146	0.1348	-0.0634	-0.1907	0.0563	0.321	0.0933	-0.2086	-0.0709	0.1725	0.0004	-0.0962	0.1153	-0.002	0.1067	-30.2003	-18.2832	-39.2071
6	0.421	0.0115	0.3795	0.8086	0.0331	0.4138	-0.0038	0.0583	-0.0354	0.0238	0.0167	-0.0252	0.0334	-0.0093	-0.0129	0.1039	-0.0062	-0.0203	0.0758	-0.0233	0.0323	-10.0452	-7.4248	-21.2364
7	3.3197	-1.2127	0.0917	1.8222	1.3248	1.6136	0.1692	0.3258	-0.177	-0.0492	-0.0167	-0.1151	0.0636	0.1275	-0.1525	0.1539	0.011	-0.0631	0.0414	-0.0248	0.0601	-5.0688	-21.6314	-18.7788
8	1.8158	-0.6689	0.4284	2.0428	-0.2163	1.4053	0.1447	0.3191	-0.1255	-0.2661	-0.0359	-0.0768	0.1745	0.1985	-0.1088	0.1706	-0.002	-0.0537	0.1665	-0.0769	0.0765	-13.7916	-19.9336	-38.0082
9	2.4492	0.8524	-1.0334	1.9644	-0.6478	1.2154	-0.0494	-0.0432	0.0655	-0.0032	0.0191	-0.3923	-0.0681	0.2969	0.0303	0.1532	0.0019	0.0276	0.1696	-0.031	0.1391	44.4462	23.0941	-23.2236
10	0.5064	0.0429	-0.2289	0.5414	0.0622	0.1871	0.0322	0.1028	-0.0117	-0.0089	-0.0267	-0.0123	-0.0232	0.0152	-0.0055	0.0862	-0.0046	-0.0172	0.0867	-0.005	0.0177	17.4178	13.192	-14.2727
11	4.6194	-0.6877	0.9745	1.0709	-1.3352	4.1473	0.1237	0.5962	0.1659	-0.0414	-0.0327	0.0562	0.1226	0.0002	-0.091	0.1049	0.0036	0.0172	0.0836	0.0311	0.043	10.7397	28.6108	-18.2746
12	1.956	-0.5831	-0.4204	2.147	-0.3292	1.0844	0.0719	0.3898	0.0525	-0.2294	0.0038	-0.0152	-0.0059	-0.0391	-0.0757	0.1375	-0.0469	0.0398	0.1375	0.0254	0.0693	28.1661	24.1653	-29.1604
13	1.4836	-0.5395	-0.8165	1.8818	1.2572	2.5179	-0.0046	0.1294	-0.0385	-0.2127	0.0201	-0.1929	0.0807	0.1991	-0.0155	0.1769	0.0447	0.0359	0.1042	-0.0104	0.1786	38.5857	-18.0962	-30.674
14	0.7696	-0.1024	-0.4049	0.8204	-0.1639	0.3887	-0.019	0.042	-0.043	0.0015	0.0003	-0.071	0.0573	0.0369	0.0187	0.1044	0.0225	-0.0338	0.0527	-0.0287	0.0315	20.0721	-8.9457	-10.1809
15	3.4903	-1.317	-0.5847	1.169	-0.7737	1.6739	-0.0162	-0.3122	-0.0578	0.1079	-0.1067	-0.0983	0.0002	0.414	0.1229	0.2945	0.0238	-0.0261	0.1128	0.0312	0.1597	26.4633	-24.1533	-1.589
16	1.1451	-0.2175	-0.4349	1.7683	-0.4635	1.0763	-0.0316	-0.0976	-0.0498	-0.0497	-0.0448	-0.3437	0.0764	0.3559	0.0764	0.1418	0.0573	0.0142	0.1607	-0.0484	0.1748	38.9336	-18.2804	-17.9838
17	0.9055	0.3361	0.8121	2.3439	1.4022	2.8479	-0.0201	-0.1684	0.0297	0.2813	0.0434	0.0116	-0.0381	0.0506	-0.0233	0.1032	0.0357	-0.0245	0.0858	-0.0108	0.0531	51.4379	36.3292	-60.9065
18	0.4316	-0.1958	0.4865	0.8269	0.1621	0.7544	-0.0034	0.0255	-0.003	-0.0448	0.0362	-0.039	-0.0206	0.0778	-0.0328	0.0876	0.005	-0.0207	0.0719	-0.0171	0.0106	42.0318	26.5837	-86.8256
19	3.9092	1.1352	0.7396	1.0616	-0.5825	2.5476	-0.0217	0.239	-0.1274	-0.1162	-0.0323	-0.1562	-0.0991	0.4272	0.054	0.168	-0.0376	-0.0235	0.0781	0.0052	0.0453	50.7138	42.3526	-91.9361
20	0.9391	0.1921	0.3448	1.9608	-0.406	1.57	-0.0411	0.0506	0.0349	0.0863	0.0211	-0.1988	-0.0236	0.2944	0.02	0.1049	0.009	-0.0429	0.13	-0.0478	0.0545	56.8747	36.3621	-73.0732
21	0.8838	-0.0411	0.9748	0.8017	-0.2944	1.4965	0.0127	-0.1402	-0.0814	0.1366	0.0375	-0.0783	0.0271	0.0039	-0.0502	0.1272	0.0206	-0.0542	0.1152	0.0119	0.044	49.1276	0.8618	-71.8455
22	2.108	1.5137	1.6551	3.4559	-0.6284	2.6931	0.157	-0.2113	0.0098	0.1248	0.0604	0.3147	0.0983	-0.3235	-0.2173	0.096	0.0311	-0.0394	0.0616	0.0033	0.0611	34.255	1.2095	-90.5407
23	2.3588	0.6874	-0.1425	1.4345	-0.7422	3.247	0.2046	-0.4274	-0.1767	0.1476	-0.0186	0.281	0.0646	-0.4122	-0.186	0.1641	-0.051	-0.0749	0.1397	0.0672	0.1567	28.5415	-10.5802	-76.7421
24	1.205	0.1762	0.4257	1.6143	-0.094	1.2262	0.0387	-0.3169	-0.0764	0.3064	0.0508	-0.113	0.0838	-0.0399	-0.0896	0.1511	0.0259	-0.074	0.1423	0.0423	0.0752	48.3468	-4.0331	-65.2682
25	1.9969	-0.7758	-0.5671	2.7435	0.1124	1.1413	0.0249	0.0015	0.1266	0.1787	-0.0267	0.6829	-0.0238	-0.3506	0.0017	0.1972	0.0169	0.1213	0.3029	-0.0398	0.288	-15.7358	36.5682	-82.3426
26	0.2991	0.0016	-0.2134	1.0583	0.0942	0.1895	0.0392	-0.0409	-0.0125	0.0785	-0.0467	0.0759	-0.0218	-0.038	0.0075	0.089	0.0105	-0.0109	0.1512	0.0094	0.019	10.4929	27.2095	-90.8102
27	3.0965	0.4661	0.0028	1.2972	0.8667	3.6244	0.1261	-0.3724	0.2098	0.1803	-0.0759	-0.0298	-0.1088	-0.1169	-0.0502	0.1346	0.0064	0.0282	0.0628	-0.0472	0.0961	16.2527	44.7157	-85.468
28	1.5897	0.7518	-0.3993	2.4481	0.0313	0.9124	0.1054	-0.3912	0.0718	0.3962	-0.0809	0.2193	0.0039	-0.0737	-0.0245	0.1816	0.0416	0.0966	0.2576	-0.0544	0.1164	-1.7347	36.6624	-75.8438
29	1.798	0.3381	-0.5074	2.0653	-0.0762	0.6588	-0.0617	-0.3478	-0.1889	0.5088	-0.0202	0.4369	0.0516	-0.2753	0.0819	0.2721	-0.0561	0.1382	0.3657	0.035	0.3026	-11.5098	-4.5621	-75.1317
30	0.2378	-0.0972	0.0438	1.0944	0.2739	0.7274	0.0311	-0.0022	-0.0786	0.0471	-0.041	0.1493	0.0485	-0.2292	0.0099	0.0951	-0.0271	-0.0191	0.0856	0.0104	0.0525	7.909	4.9448	-94.9053
31	3.9915	0.9542	1.1416	1.8756	0.7256	4.8651	-0.0429	0.2304	-0.069	-0.1118	-0.1236	0.2413	0.0614	-0.4569	0.1665	0.1534	-0.029	-0.0254	0.0992	-0.0112	0.1327	5.7741	-11.9007	-102.6956
32	1.3426	-0.2437	-0.2211	2.4073	0.9803	1.4188	-0.0247	0.096	-0.1381	0.048	-0.1069	0.5329	0.059	-0.3595	0.1317	0.1071	-0.0923	0.0533	0.2263	0.0279	0.2855	-10.6437	-4.9564	-90.3132

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	45 - 126
2	X-RAY DIFFRACTION	2	A	127 - 250
3	X-RAY DIFFRACTION	3	A	251 - 267
4	X-RAY DIFFRACTION	4	A	268 - 480
5	X-RAY DIFFRACTION	5	B	47 - 127
6	X-RAY DIFFRACTION	6	B	128 - 231
7	X-RAY DIFFRACTION	7	B	232 - 306
8	X-RAY DIFFRACTION	8	B	307 - 480
9	X-RAY DIFFRACTION	9	C	46 - 124
10	X-RAY DIFFRACTION	10	C	125 - 249
11	X-RAY DIFFRACTION	11	C	250 - 310
12	X-RAY DIFFRACTION	12	C	311 - 480
13	X-RAY DIFFRACTION	13	D	46 - 127
14	X-RAY DIFFRACTION	14	D	128 - 251
15	X-RAY DIFFRACTION	15	D	252 - 348
16	X-RAY DIFFRACTION	16	D	349 - 480
17	X-RAY DIFFRACTION	17	E	46 - 127
18	X-RAY DIFFRACTION	18	E	128 - 244
19	X-RAY DIFFRACTION	19	E	245 - 345
20	X-RAY DIFFRACTION	20	E	346 - 480
21	X-RAY DIFFRACTION	21	F	47 - 206
22	X-RAY DIFFRACTION	22	F	207 - 256
23	X-RAY DIFFRACTION	23	F	257 - 361
24	X-RAY DIFFRACTION	24	F	362 - 480
25	X-RAY DIFFRACTION	25	G	46 - 127
26	X-RAY DIFFRACTION	26	G	128 - 250
27	X-RAY DIFFRACTION	27	G	251 - 322
28	X-RAY DIFFRACTION	28	G	323 - 480
29	X-RAY DIFFRACTION	29	H	47 - 126
30	X-RAY DIFFRACTION	30	H	127 - 250
31	X-RAY DIFFRACTION	31	H	251 - 319
32	X-RAY DIFFRACTION	32	H	320 - 480

-
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

-
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