PDB-2y9x: Crystal structure of PPO3, a tyrosinase from Agaricus bisporus, i...

ID or keywords:

Entry

Database: PDB / ID: 2y9x

Title

Crystal structure of PPO3, a tyrosinase from Agaricus bisporus, in deoxy-form that contains additional unknown lectin-like subunit, with inhibitor tropolone

Components

LECTIN-LIKE FOLD PROTEIN
POLYPHENOL OXIDASE

Keywords

OXIDOREDUCTASE / COPPER-CONTAINING / PIGMENTATION / TYPE-3 COPPER PROTEIN

Function / homology

Function and homology information

tyrosinase / tyrosinase activity / melanin biosynthetic process / metal ion binding
Similarity search - Function

Biological species

AGARICUS BISPORUS (button mushroom)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.78 Å

Authors

Ismaya, W.T. / Rozeboom, H.J. / Weijn, A. / Mes, J.J. / Fusetti, F. / Wichers, H.J. / Dijkstra, B.W.

Citation

Journal: Biochemistry / Year: 2011
Title: Crystal Structure of Agaricus Bisporus Mushroom Tyrosinase: Identity of the Tetramer Subunits and Interaction with Tropolone.
Authors: Ismaya, W.T. / Rozeboom, H.J. / Weijn, A. / Mes, J.J. / Fusetti, F. / Wichers, H.J. / Dijkstra, B.W.

History

Deposition	Feb 17, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 6, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 30, 2019	Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type Item: _pdbx_database_status.status_code_sf
Revision 1.3	Dec 20, 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_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.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_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	2y9x.cif.gz	832.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2y9x.ent.gz	693.7 KB	Display	PDB format
PDBx/mmJSON format	2y9x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2y9x_validation.pdf.gz	517.6 KB	Display	wwPDB validaton report
Full document	2y9x_full_validation.pdf.gz	538.9 KB	Display
Data in XML	2y9x_validation.xml.gz	68.7 KB	Display
Data in CIF	2y9x_validation.cif.gz	92.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y9/2y9x ftp://data.pdbj.org/pub/pdb/validation_reports/y9/2y9x	HTTPS FTP

-
Related structure data

Related structure data	2y9wSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2y9w-2 2y9w-1 5aja-d 4hr0-1 3uek-d 4xze-4 1brl-2 2j5u-d 1xpr-1 6tbj-4 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) 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

2y9wSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: POLYPHENOL OXIDASE

B: POLYPHENOL OXIDASE

C: POLYPHENOL OXIDASE

D: POLYPHENOL OXIDASE

E: LECTIN-LIKE FOLD PROTEIN

F: LECTIN-LIKE FOLD PROTEIN

G: LECTIN-LIKE FOLD PROTEIN

H: LECTIN-LIKE FOLD PROTEIN

hetero molecules

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

1

A: POLYPHENOL OXIDASE

E: LECTIN-LIKE FOLD PROTEIN

hetero molecules

defined by author&software
62.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: POLYPHENOL OXIDASE

F: LECTIN-LIKE FOLD PROTEIN

hetero molecules

defined by author&software
62.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: POLYPHENOL OXIDASE

G: LECTIN-LIKE FOLD PROTEIN

hetero molecules

defined by author&software
62.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: POLYPHENOL OXIDASE

H: LECTIN-LIKE FOLD PROTEIN

hetero molecules

defined by author&software
62.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.840, 104.820, 119.360
Angle α, β, γ (deg.)	90.00, 110.45, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
1	2	E
2	2	F
3	2	G
4	2	H

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	5 - 390
2	1	1	4	B	5 - 390
3	1	1	4	C	5 - 390
4	1	1	4	D	5 - 390
1	1	2	4	E	5 - 150
2	1	2	4	F	5 - 150
3	1	2	4	G	5 - 150
4	1	2	4	H	5 - 150

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.9999, 0.000622, -0.01034), (-0.000625, -1, 0.000312), (-0.01034, 0.000318, 0.9999)	-10.67, -1.515, -0.0612
2	given	(0.07056, 0.9975, -0.006027), (0.9972, -0.07068, -0.0231), (-0.02347, -0.004381, -0.9997)	-4.485, 2.047, -136.2
3	given	(-0.07034, -0.9975, -0.008863), (-0.9972, 0.07055, -0.02639), (0.02695, 0.006982, -0.9996)	-6.965, -8.218, -135.9
4	given	(-1, -0.000673, -0.001914), (0.00067, -1, 0.001431), (-0.001915, 0.00143, 1)	-10.27, -1.47, -0.1585
5	given	(0.0596, 0.9982, -0.003095), (0.9982, -0.05968, -0.002964), (-0.003143, -0.002913, -1)	-4.252, 4.09, -136
6	given	(-0.06252, -0.998, -0.007508), (-0.998, 0.06258, -0.007527), (0.007982, 0.007022, -0.9999)	-6.768, -6.315, -135.9

-
Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein	POLYPHENOL OXIDASE / TYROSINASE Mass: 45318.617 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-392 / Source method: isolated from a natural source / Details: COMMERCIAL / Source: (natural) AGARICUS BISPORUS (button mushroom) / References: UniProt: C7FF04, tyrosinase
#2: Protein	LECTIN-LIKE FOLD PROTEIN Mass: 16478.287 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: COMMERCIAL / Source: (natural) AGARICUS BISPORUS (button mushroom) / References: UniProt: G1K3P4*PLUS

-
Non-polymers , 4 types, 41 molecules

#3: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#4: Chemical	ChemComp-HO / HOLMIUM ATOM Mass: 164.930 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ho
#5: Chemical	ChemComp-0TR / 2-HYDROXYCYCLOHEPTA-2,4,6-TRIEN-1-ONE / TROPOLONE Mass: 122.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₇H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Sequence details	NO DATABASE REFERENCE ORF 239342 OF A. BISPORUS GENOME CONSORTIUM.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.5 % / Description: NONE
Crystal grow	pH: 4.6 Details: 10% PEG 4000, 100 MM NA ACETATE PH 4.6, 5 MM HOLMIUM CHLORIDE.

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 2.78→58 Å / Num. obs: 54004 / % possible obs: 89.6 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / R_merge(I) obs: 0.24 / Net I/σ(I): 3.5
Reflection shell	Resolution: 2.78→2.93 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.62 / Mean I/σ(I) obs: 1.6 / % possible all: 89.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y9W

2y9w

Resolution: 2.78→58.03 Å / Cor.coef. F_o:F_c: 0.87 / Cor.coef. F_o:F_c free: 0.802 / SU B: 42.963 / SU ML: 0.398 / Cross valid method: THROUGHOUT / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.289	2715	5 %	RANDOM
R_work	0.235	-	-	-
obs	0.238	51269	89.1 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 52.7 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.13 Å²	0 Å²	-0.03 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	-0.17 Å²

Refinement step

Cycle: LAST / Resolution: 2.78→58.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17052	0	48	25	17125

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	17662
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.95	1.922	24036
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.979	5	2096
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.557	24.578	900
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.646	15	2716
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.274	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	2472
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	13912
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	0.143	1.5	10492
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.266	2	16956
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.491	3	7170
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.533	4.5	7080
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	3168	medium positional	0.22	0.5
1	2	B	3168	medium positional	0.23	0.5
1	3	C	3168	medium positional	0.23	0.5
1	4	D	3168	medium positional	0.23	0.5
2	1	E	1056	medium positional	0.28	0.5
2	2	F	1056	medium positional	0.29	0.5
2	3	G	1056	medium positional	0.34	0.5
2	4	H	1056	medium positional	0.28	0.5
1	1	A	3168	medium thermal	0.14	2
1	2	B	3168	medium thermal	0.14	2
1	3	C	3168	medium thermal	0.13	2
1	4	D	3168	medium thermal	0.15	2
2	1	E	1056	medium thermal	0.11	2
2	2	F	1056	medium thermal	0.11	2
2	3	G	1056	medium thermal	0.11	2
2	4	H	1056	medium thermal	0.11	2

LS refinement shell

Resolution: 2.78→2.85 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.385	211	-
R_work	0.308	3679	-
obs	-	-	87.57 %

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	1.4605	-0.0727	-0.4112	1.452	-0.4404	0.7377	-0.0897	-0.0982	0.0306	0.1818	0.0502	0.0439	-0.0362	-0.1105	0.0395	0.1145	-0.014	0.0366	0.0615	-0.0276	0.0231	-13.1883	-20.7885	-25.5832
2	0.6829	0.374	0.1693	1.0853	-0.1139	0.9411	-0.1055	0.0418	-0.1258	-0.1311	0.0292	-0.221	0.277	0.0209	0.0763	0.1408	0.0384	0.0488	0.0857	0.0005	0.1262	-4.8428	-34.8812	-32.4316
3	1.4808	1.7717	-0.1246	4.9989	-0.7986	0.1746	0.0091	0.1629	0.0197	-0.4348	0.0163	0.0864	0.1234	0.0027	-0.0255	0.1115	0.0094	0.0058	0.139	-0.0016	0.0447	-6.0719	-28.6294	-41.6669
4	1.1054	0.2438	-0.049	1.3214	-0.3128	1.0576	0.0131	0.1319	0.0512	0.1577	-0.0946	-0.0787	-0.079	0.1366	0.0815	0.0676	-0.0202	0.0326	0.0408	0.0202	0.0572	-2.4811	-10.8709	-37.3733
5	0.7781	-0.0055	0.6989	1.1518	0.668	1.0249	-0.074	-0.0081	0.0529	0.2709	0.0868	-0.1035	0.0994	0.0646	-0.0128	0.1527	-0.0077	-0.0281	0.0964	0.0212	0.0691	2.8046	19.2561	-25.4999
6	0.8181	0.2128	-0.2167	1.5201	0.7803	0.864	-0.0828	0.0879	0.3276	-0.1186	0.0662	0.2066	-0.1756	0.0347	0.0165	0.1761	0.0303	-0.0459	0.046	0.0479	0.1457	-5.4884	33.2968	-32.455
7	1.0355	1.147	0.2361	2.1969	-0.2684	1.6891	-0.0598	0.3082	0.0985	-0.1407	0.0781	0.1533	-0.1695	0.0127	-0.0183	0.087	0.0275	0.0103	0.2143	0.053	0.1089	-4.9964	25.868	-41.5108
8	2.0876	0.2701	-0.0192	0.5314	0.2559	1.5536	0.022	0.0358	0.1613	0.1343	0.0305	0.0604	0.0736	-0.0949	-0.0525	0.1381	-0.013	-0.0212	0.0145	0.0222	0.0731	-7.3646	9.332	-37.2935
9	0.6523	-0.3745	0.0263	1.9737	0.2057	0.811	0.049	0.4173	-0.1194	-0.3119	-0.0436	0.1519	0.2046	0.0163	-0.0054	0.1463	0.0132	-0.0661	0.3077	-0.1029	0.1145	-25.9694	-7.5665	-110.0517
10	0.622	0.3485	-0.0041	0.7429	0.4618	0.4101	0.0818	0.2704	-0.1283	-0.126	-0.1113	0.0314	-0.1246	-0.2397	0.0294	0.1604	0.0204	-0.1096	0.3507	-0.0634	0.2181	-39.3026	1.7847	-102.8697
11	4.8039	1.2008	0.5829	1.0998	0.3415	0.1215	0.0801	-0.0612	-0.1111	-0.0424	-0.1556	0.1956	-0.0164	-0.0452	0.0755	0.1361	0.0071	-0.0443	0.099	-0.0183	0.1947	-31.6932	0.9363	-93.9827
12	0.9136	0.2398	0.2676	2.7683	0.1416	0.6229	0.0919	0.1902	-0.0788	-0.1611	0.057	0.0695	-0.126	-0.0445	-0.1488	0.0639	0.0517	0.0193	0.1352	-0.0366	0.0677	-14.9802	2.0474	-98.6417
13	0.5953	0.0734	-0.0182	0.991	-0.1704	0.7262	-0.0163	0.3206	0.1188	-0.2651	-0.0004	-0.034	-0.2014	0.1129	0.0167	0.1884	-0.0046	0.0121	0.2654	0.042	0.063	15.9351	6.1132	-109.9186
14	0.7175	0.1524	0.6321	1.5413	-0.3672	0.7509	0.0599	0.2219	-0.0525	-0.0424	-0.0614	-0.2348	0.0318	0.2737	0.0016	0.0952	0.0179	0.0765	0.242	0.0229	0.1014	29.2691	-3.2594	-102.7844
15	5.8383	1.9962	0.2743	2.0152	0.4598	0.1502	-0.0347	-0.0078	0.008	0.0236	0.0079	-0.042	0.0624	0.0321	0.0268	0.1148	0.0348	0.015	0.0966	0.0041	0.0938	21.3625	-2.5944	-93.8848
16	0.5702	0.3982	-0.2471	1.1715	-0.0429	0.4201	0.0039	0.1613	-0.0202	-0.0655	0.0908	-0.0381	0.0424	0.076	-0.0947	0.0821	0.0312	-0.0353	0.1434	-0.0195	0.0956	4.9507	-3.4326	-98.6646
17	0.9337	-1.1062	2.3324	3.2887	-2.0396	6.1077	-0.0049	0.1487	0.1387	-0.0722	-0.4264	0.1582	-0.1117	0.2648	0.4313	0.0398	0.0175	0.0453	0.0724	0.0106	0.2206	-22.3119	-5.2006	-65.2291
18	0.6002	0.0925	-0.5772	2.4463	-0.2476	2.4191	0.1306	-0.1931	-0.025	-0.2178	-0.1611	0.0625	-0.4812	0.0121	0.0305	0.1286	0.0128	-0.031	0.1399	-0.0699	0.138	-22.9761	-0.1594	-57.6593
19	3.777	-0.7637	-0.9863	3.431	-0.4291	4.7553	0.0941	-0.0877	-0.1118	-0.1636	-0.1346	0.4244	0.0974	-0.3853	0.0405	0.0509	-0.0485	-0.0528	0.1455	-0.0381	0.1392	-34.5911	-6.6861	-57.3103
20	4.7504	1.6013	-1.5858	1.0447	-0.4737	6.3061	0.2551	-0.0215	0.3634	-0.1597	-0.0862	-0.1281	0.1798	-0.1231	-0.1689	0.1804	0.0548	0.0906	0.0286	0.0167	0.2141	12.2034	3.5314	-65.0251
21	0.3187	0.2179	0.4266	4.5275	-0.7727	1.0306	0.1603	-0.1168	-0.1043	-0.2055	-0.199	-0.1897	0.4396	-0.0631	0.0387	0.2114	-0.0014	0.0655	0.1434	0.0891	0.1511	12.8321	-1.3558	-57.4707
22	6.024	-1.1852	-0.2861	3.2426	0.6222	0.465	0.125	-0.132	-0.1119	-0.1428	-0.061	-0.3391	-0.2363	0.0744	-0.064	0.1517	-0.0241	0.0346	0.1733	0.0126	0.0763	24.4168	5.1095	-57.0801
23	1.6725	1.5901	-2.4847	1.8001	-2.4785	5.6927	-0.2697	-0.0271	0.0087	-0.0157	0.1162	0.2225	-0.2904	0.4954	0.1535	0.3687	-0.0227	0.0813	0.2336	0.1957	0.198	-10.544	-17.6819	-70.7219
24	2.0209	0.1717	0.148	2.9321	1.3469	0.6522	-0.0816	-0.117	-0.1521	0.017	0.1411	-0.1386	0.0074	0.1369	-0.0595	0.1602	0.0066	0.0456	0.1737	0.0551	0.0561	-5.6292	-18.6689	-78.2662
25	3.2254	-0.3099	1.7794	1.1657	1.2138	3.1562	0.0289	-0.0737	-0.6021	0.1219	0.0158	0.1381	0.4678	-0.0888	-0.0447	0.2411	-0.0638	0.0877	0.0307	0.0178	0.2153	-12.8042	-29.8338	-78.5012
26	2.2237	-3.141	1.1967	4.7165	-0.4541	7.0594	-0.2115	-0.3335	-0.2113	0.1567	0.2866	0.3069	-0.1409	-0.4054	-0.0751	0.0589	0.0712	0.0731	0.2101	-0.0027	0.1709	0.4123	16.0774	-70.6465
27	1.815	0.24	-0.0884	1.9118	-1.4491	1.4586	-0.1121	-0.1109	0.2777	-0.0589	0.0751	0.0848	0.1093	-0.3277	0.037	0.1371	-0.0268	-0.057	0.2046	-0.093	0.0976	-4.4831	17.1124	-78.2198
28	6.1983	-0.4985	0.2558	4.0052	1.0238	0.45	-0.2016	0.0292	0.5135	0.1213	0.2252	-0.0122	-0.2002	0.122	-0.0236	0.3133	-0.0619	0.0212	0.0544	-0.0255	0.1309	2.6728	28.2891	-78.4112

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 136
2	X-RAY DIFFRACTION	2	A	137 - 240
3	X-RAY DIFFRACTION	3	A	241 - 305
4	X-RAY DIFFRACTION	4	A	306 - 393
5	X-RAY DIFFRACTION	5	B	2 - 136
6	X-RAY DIFFRACTION	6	B	137 - 240
7	X-RAY DIFFRACTION	7	B	241 - 309
8	X-RAY DIFFRACTION	8	B	310 - 393
9	X-RAY DIFFRACTION	9	C	2 - 136
10	X-RAY DIFFRACTION	10	C	137 - 240
11	X-RAY DIFFRACTION	11	C	241 - 309
12	X-RAY DIFFRACTION	12	C	310 - 393
13	X-RAY DIFFRACTION	13	D	2 - 136
14	X-RAY DIFFRACTION	14	D	137 - 240
15	X-RAY DIFFRACTION	15	D	241 - 310
16	X-RAY DIFFRACTION	16	D	311 - 393
17	X-RAY DIFFRACTION	17	E	9 - 41
18	X-RAY DIFFRACTION	18	E	42 - 100
19	X-RAY DIFFRACTION	19	E	101 - 150
20	X-RAY DIFFRACTION	20	F	9 - 41
21	X-RAY DIFFRACTION	21	F	42 - 100
22	X-RAY DIFFRACTION	22	F	101 - 150
23	X-RAY DIFFRACTION	23	G	9 - 41
24	X-RAY DIFFRACTION	24	G	42 - 100
25	X-RAY DIFFRACTION	25	G	101 - 150
26	X-RAY DIFFRACTION	26	H	9 - 41
27	X-RAY DIFFRACTION	27	H	42 - 100
28	X-RAY DIFFRACTION	28	H	101 - 150

-
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 , 2 types, 8 molecules ABCDEFGH

-
Non-polymers , 4 types, 41 molecules

-
Details

-
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 , 2 types, 8 molecules ABCDEFGH

-Non-polymers , 4 types, 41 molecules

-Details

-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 , 2 types, 8 molecules ABCDEFGH

-
Non-polymers , 4 types, 41 molecules

-
Details

-
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