PDB-2wyr: 3-D structure of PhTET1-12s, dodecamer in the asymmetric unit

ID or keywords:

Entry

Database: PDB / ID: 2wyr

Title

3-D structure of PhTET1-12s, dodecamer in the asymmetric unit

Components

COBALT-ACTIVATED PEPTIDASE TET1

Keywords

HYDROLASE / LARGE SELF-ASSEMBLED DODECAMER / HYPERTHERMOPHILIC

Function / homology

Function and homology information

aminopeptidase activity / proteolysis / metal ion binding
Similarity search - Function

Biological species

PYROCOCCUS HORIKOSHII (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.245 Å

Authors

Vellieux, F.M.D. / Dura, M.A. / Franzetti, B.

Citation

Journal: To be Published
Title: Structure of Phtet1-12S, Dodecamer in the Asymmetric Unit
Authors: Dura, M.A. / Vellieux, F.M.D.

History

Deposition	Nov 20, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 1, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	May 8, 2019	Group: Data collection / Experimental preparation / Other Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4	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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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
Revision 1.5	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2wyr.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb2wyr.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	2wyr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2wyr_validation.pdf.gz	520 KB	Display	wwPDB validaton report
Full document	2wyr_full_validation.pdf.gz	588.7 KB	Display
Data in XML	2wyr_validation.xml.gz	149.2 KB	Display
Data in CIF	2wyr_validation.cif.gz	205.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wy/2wyr ftp://data.pdbj.org/pub/pdb/validation_reports/wy/2wyr	HTTPS FTP

-
Related structure data

Related structure data	2cf4S S: Starting model for refinement
Similar structure data	2cf4-1 2gre-1 2gre-2 4wwv-1 1xfo-1 1y0r-1 3kl9-d 1y0y-1 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	#104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: COBALT-ACTIVATED PEPTIDASE TET1

B: COBALT-ACTIVATED PEPTIDASE TET1

C: COBALT-ACTIVATED PEPTIDASE TET1

D: COBALT-ACTIVATED PEPTIDASE TET1

E: COBALT-ACTIVATED PEPTIDASE TET1

F: COBALT-ACTIVATED PEPTIDASE TET1

G: COBALT-ACTIVATED PEPTIDASE TET1

H: COBALT-ACTIVATED PEPTIDASE TET1

I: COBALT-ACTIVATED PEPTIDASE TET1

J: COBALT-ACTIVATED PEPTIDASE TET1

K: COBALT-ACTIVATED PEPTIDASE TET1

L: COBALT-ACTIVATED PEPTIDASE TET1

hetero molecules

445 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	113.263, 205.218, 113.488
Angle α, β, γ (deg.)	90.00, 100.78, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	COBALT-ACTIVATED PEPTIDASE TET1 / M42 AMINOPEPTIDASE / PHTET1-12S / PH0519 Mass: 36972.609 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS HORIKOSHII (archaea) / Strain: OT3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CODON PLUS (DE3)-RIL References: UniProt: O58255, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Chemical	... ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Co
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1506 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.97 Å³/Da / Density % sol: 59 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP. MOTHER LIQUOR: 1 ML OF 0.1 M TRIS-HCL, PH 7.5, 20% (W/V) PEG 3350, 0.2 M TRIMETHYLAMINE N-OXIDE. DROP: 2 UL OF MOTHER LIQUOR PLUS 2 UL OF A 6.2 MG/ML PROTEIN SOLUTION IN 20 MM ...Details: HANGING DROP. MOTHER LIQUOR: 1 ML OF 0.1 M TRIS-HCL, PH 7.5, 20% (W/V) PEG 3350, 0.2 M TRIMETHYLAMINE N-OXIDE. DROP: 2 UL OF MOTHER LIQUOR PLUS 2 UL OF A 6.2 MG/ML PROTEIN SOLUTION IN 20 MM TRIS-HCL, 150 MM NACL, PH 7.5. CRYSTALS AFTER 2 WEEKS. CRYOPROTECTING SOLUTION: 0.1 M TRIS-HCL, PH 7.5, 20% (W/V) PEG 3350, 0.2 M TRIMETHYLAMINE N-OXIDE, 20% (V/V) ETHYLENE GLYCOL

Crystal

Density Matthews: 2.97 Å³/Da / Density % sol: 59 % / Description: NONE

Crystal grow

Method: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP. MOTHER LIQUOR: 1 ML OF 0.1 M TRIS-HCL, PH 7.5, 20% (W/V) PEG 3350, 0.2 M TRIMETHYLAMINE N-OXIDE. DROP: 2 UL OF MOTHER LIQUOR PLUS 2 UL OF A 6.2 MG/ML PROTEIN SOLUTION IN 20 MM ...

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
Detector	Type: ADSC CCD / Detector: CCD / Date: Jun 18, 2006 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.24→111.48 Å / Num. obs: 1810946 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / B_iso Wilson estimate: 32.9 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 17.8
Reflection shell	Resolution: 2.24→2.38 Å / Redundancy: 7.45 % / R_merge(I) obs: 0.47 / Mean I/σ(I) obs: 4.63 / % possible all: 95.1

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
TRUNCATE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CF4, DODECAMER RECONSTRUCTED USING CRYSTALLOGRAPHIC SYMMETRY OPERATORS

2cf4

Resolution: 2.245→49.684 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 21.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2199	12097	5 %
R_work	0.1702	-	-
obs	0.1726	241259	99.77 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 39.608 Å² / k_sol: 0.349 e/Å³

Displacement parameters

B_iso mean: 35.85 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.1793 Å²	0 Å²	-1.1682 Å²
2-	-	-2.5972 Å²	-0 Å²
3-	-	-	4.7765 Å²

Refinement step

Cycle: LAST / Resolution: 2.245→49.684 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30577	0	24	1506	32107

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	31348
X-RAY DIFFRACTION	f_angle_d	1.205	42309
X-RAY DIFFRACTION	f_dihedral_angle_d	17.961	11585
X-RAY DIFFRACTION	f_chiral_restr	0.085	4845
X-RAY DIFFRACTION	f_plane_restr	0.004	5392

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.245-2.3253	0.2716	1182	0.2045	22619	X-RAY DIFFRACTION	98
2.3253-2.4184	0.2621	1215	0.1872	22890	X-RAY DIFFRACTION	100
2.4184-2.5284	0.2576	1189	0.1889	22943	X-RAY DIFFRACTION	100
2.5284-2.6617	0.2525	1244	0.1852	22863	X-RAY DIFFRACTION	100
2.6617-2.8285	0.2425	1162	0.1799	22997	X-RAY DIFFRACTION	100
2.8285-3.0468	0.2441	1218	0.1806	22896	X-RAY DIFFRACTION	100
3.0468-3.3534	0.2241	1247	0.1749	22945	X-RAY DIFFRACTION	100
3.3534-3.8385	0.2096	1219	0.1628	22929	X-RAY DIFFRACTION	100
3.8385-4.8354	0.1756	1187	0.1405	23016	X-RAY DIFFRACTION	100
4.8354-49.6965	0.1946	1234	0.158	23064	X-RAY DIFFRACTION	100

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	0.2176	0.4204	-0.2312	0.1262	-0.3886	0.6116	-0.0586	0.0094	-0.0738	-0.0195	-0.0152	-0.0883	0.159	0.0833	0	0.1102	0.0421	0.0198	0.0961	-0.0267	0.1165	40.5309	-40.2331	33.5176
2	0.1143	0.2345	-0.0038	0.1268	-0.1643	0.2178	0.0769	-0.0516	-0.063	0.0703	-0.0476	0.0336	-0.0939	0.0705	-0	0.111	0.0004	-0.0005	0.0937	0.0086	0.1176	31.5759	-30.2223	52.6053
3	0.2771	0.0543	0.08	0.0479	-0.108	0.5668	-0.0218	0.0608	-0.0838	-0.0349	0.0192	-0.0332	0.0281	0.0326	0	0.1568	-0.0097	0.0185	0.1382	-0.0227	0.103	32.5716	-36.555	25.3146
4	0.0197	-0.012	-0.0028	0.0377	0.039	0.0247	0.1107	-0.0278	-0.2915	-0.2851	-0.108	0.0883	0.344	-0.0975	-0	0.334	-0.006	0.0335	0.2174	-0.1135	0.2033	30.3393	-45.9218	13.8168
5	0.0814	-0.2173	0.3918	0.1906	-0.0468	0.1084	-0.0055	-0.2019	0.2393	0.3505	0.2039	-0.5391	0.1484	-0.0275	-0	0.2026	-0.0962	0.0751	0.1921	0.0853	-0.3503	3.9309	-17.5773	92.666
6	0.364	-0.0018	0.0985	0.1571	0.1725	-0.0102	0.001	0.0361	0.013	0.016	0.0232	-0.0192	-0.0284	0.0276	-0	0.185	-0.0468	0.0037	0.1572	-0.0128	0.0682	23.2543	-8.6888	78.1437
7	0.159	-0.0057	-0.0602	0.4801	-0.0711	0.2742	0.1059	-0.0226	0.0442	0.1474	-0.0723	-0.097	0.0011	-0.0938	0	0.2205	-0.0657	0.0132	0.2102	-0.0274	0.0455	8.2215	-10.54	90.4657
8	0.527	0.1044	0.2324	0.3211	-0.1586	0.2057	0.0541	-0.0702	0.0581	-0.007	-0.0648	0.0406	0.0147	-0.048	0	0.1876	-0.0609	0.067	0.1966	-0.0346	0.0867	-9.0785	-11.6609	82.8596
9	0.157	-0.2001	-0.1716	0.3464	0.1673	0.0526	0.0112	0.0181	-0.0916	0.0137	-0.0636	0.0121	0.2613	-0.0785	0	0.1636	-0.0506	0.0035	0.0588	0.0215	0.0885	9.8553	-47.706	63.4247
10	0.3639	-0.1208	-0.0883	0.242	0.083	0.3347	0.0313	0.0719	-0.0137	0.0096	0.022	-0.0674	-0.0398	-0.0081	0	0.1007	-0.0093	0.0077	0.0763	0	0.086	13.5698	-32.7464	43.3055
11	0.3392	0.2739	0.08	0.1103	0.2076	0.4059	-0.0061	0.0772	-0.1463	0.0703	-0.0375	-0.0412	0.1147	-0.0505	0	0.1607	-0.0143	0.0039	0.0678	0.0232	0.1138	12.1586	-43.8084	62.7578
12	0.4282	0.3269	-0.069	0.3804	0.5216	0.5007	0.0801	-0.0493	-0.0557	0.0557	-0.0351	-0.0419	0.0058	0.0381	0	0.1728	-0.0306	-0.0215	0.1142	0.0445	0.0662	19.6831	-35.4502	76.1258
13	0.0296	0.206	-0.0504	0.667	-0.0105	0.2453	-0.0602	0.046	0.1332	-0.0933	0.0209	0.2394	0.0629	0.0022	0	0.0862	-0.0098	-0.063	0.1271	0.031	0.3086	-26.6233	5.4997	30.811
14	0.3876	0.1047	0.0166	0.4089	-0.0255	0.0453	-0.0568	0.0084	0.1376	-0.0843	0.0324	0.0618	0.0783	-0.0026	0	0.0439	-0.0071	-0.0211	0.0948	0.0205	0.1962	-22.3636	1.0455	34.5854
15	0.335	0.1	0.1645	0.3122	0.0295	0.1657	-0.0508	-0.0075	0.1731	0.0445	-0.0137	0.1076	-0.0128	0.0578	-0	0.1296	0.003	-0.0411	0.1175	0.0126	0.4033	-20.828	22.1724	40.462
16	0.0589	-0.0152	0.0099	0.0294	-0.0212	-0.0453	-0.0925	-0.178	0.2893	0.1777	-0.1253	0.3011	-0.0956	-0.272	-0	0.1177	0.0298	-0.03	0.1669	-0.0397	0.6384	-33.2874	23.346	42.6226
17	0.3536	-0.0835	0.3407	0.1668	-0.0054	0.2736	0.0394	0.1283	-0.1572	-0.1322	-0.0154	0.0811	0.0282	0.0132	0	0.1263	-0.0319	0.0445	0.1805	-0.0101	-0.0666	34.5787	-14.0602	3.3266
18	0.4322	-0.0671	0.2781	0.4675	-0.2112	0.1056	-0.0402	0.0494	-0.0188	-0.0835	0.1154	0.1082	-0.0155	-0.0046	0	0.1521	-0.0367	-0.0108	0.1956	0.0366	0.0545	14.1983	-13.3625	13.4663
19	0.4636	-0.0771	0.125	0.5148	0.0806	-0.0355	-0.0278	0.047	0.0529	-0.0493	0.0378	-0.0838	0.0029	0.0061	0	0.1459	-0.0348	0.0183	0.2267	0.0173	0.0451	44.2912	-3.4825	8.9733
20	0.0238	0.0308	-0.0657	0.0182	0.0117	0.0154	-0.0636	0.3336	0.1656	-0.4542	0.1017	-0.0936	-0.1782	0.0109	-0	0.2512	-0.05	0.0713	0.3481	0.0397	0.1433	49.7804	1.8376	0.7322
21	0.2116	-0.0811	0.1073	-0.0461	-0.0396	0.261	-0.0144	0.0605	0.2489	0.0177	-0.0136	0.0693	-0.2035	0.1428	-0	0.2012	-0.058	0.0184	0.0823	-0.0193	0.3351	25.3598	48.3534	62.8961
22	0.3132	-0.2607	-0.0591	0.1916	0.0755	0.4712	0.0392	0.1017	0.1514	0.0493	-0.038	0.0544	0.0635	0.1035	0	0.1384	-0.0209	-0.0275	0.1493	0.0525	0.2646	24.1352	34.3187	40.2198
23	0.1827	-0.0977	0.1296	-0.0742	0.0348	0.5206	0.0069	0.0153	0.1036	0.0245	0.0065	0.0801	-0.0267	0.0286	-0	0.1994	-0.0329	0.0354	0.1112	-0.0544	0.3196	19.7878	40.353	68.8674
24	0.2417	0.062	-0.0604	0.3226	-0.122	0.2945	0.0298	-0.0523	0.1241	0.0249	-0.0395	0.0664	-0.0292	0.0229	-0	0.2152	-0.0124	0.0367	0.1592	-0.0615	0.3052	15.0482	38.6426	75.2783
25	0.0625	0.0038	-0.0913	0.1499	0.0466	0.1476	0.1064	0.0361	0.0375	-0.0286	0.0671	-0.1835	-0.054	-0.0003	0	0.1062	-0.0247	0.0237	0.1794	-0.0165	0.1824	69.2443	-5.9959	33.1392
26	0.3553	-0.0426	0.1084	0.5719	0.052	-0.0049	-0.0361	0.0394	-0.0036	-0.0337	0.0271	-0.0349	-0.0355	0.037	-0	0.0598	-0.0072	0.0104	0.1089	-0.0006	0.0719	57.2488	-2.8446	33.8275
27	0.3311	0.2079	-0.0213	0.3973	-0.1166	0.0642	0.0043	0.0275	-0.0851	0.0357	0.0289	0.0394	0.0193	-0.03	0	0.1288	0.0075	-0.0053	0.1387	-0.0069	0.1628	56.0911	-25.114	41.0525
28	-0.0606	0.0535	-0.0261	0.1796	-0.11	0.2332	0.0116	0.0677	-0.081	0.1066	-0.0253	-0.0723	-0.0501	0.0887	0	0.0946	0.0039	-0.0167	0.1114	0.0024	0.139	62.5205	-16.4992	45.8085
29	0.2684	0.0175	-0.1453	0.0941	0.0427	0.2221	0.0401	0.2213	0.1251	-0.1331	0.0279	-0.0162	-0.0397	-0.0498	-0	0.2346	-0.0445	-0.0772	0.3251	0.1467	0.1815	-1.5163	11.7849	-0.3154
30	0.2816	0.0172	-0.1161	0.3239	0.0925	0.3375	-0.0311	-0.0026	0.1404	-0.0004	0.0781	-0.0011	0.0301	0.0307	0	0.1297	-0.0273	-0.01	0.1736	0.0549	0.1213	20.6318	10.3526	14.7798
31	0.4771	-0.0635	-0.1372	0.2589	-0.1473	-0.0328	-0.0338	0.1099	0.0478	-0.0989	0.035	0.096	0.0184	-0.0064	-0	0.1741	-0.0425	-0.0725	0.2562	0.0703	0.1725	-5.7537	3.3646	8.1477
32	0.0223	0.0552	0.0315	0.0361	-0.0102	0.0309	-0.0566	0.1572	-0.2266	-0.266	0.1034	0.1934	0.151	0.0638	-0	0.3231	-0.0712	-0.1308	0.4055	0.042	0.3147	-15.3351	-2.5577	-0.3136
33	0.196	-0.0934	-0.1901	0.2393	0.1876	0.1489	0.0143	0.0437	0.3059	-0.0068	-0.0232	0.1508	-0.1257	-0.1283	-0	0.1645	0.0211	-0.0834	0.163	0.1099	0.4662	-5.7831	44.4334	26.2174
34	0.3951	0.2049	0.0599	0.2206	0.1889	0.5282	-0.004	-0.0581	0.1197	0.0028	-0.0572	0.1102	0.0868	0.0013	-0	0.1461	-0.0149	-0.0003	0.1425	0.0297	0.3336	-0.7227	30.1384	50.8466
35	0.4384	0.2144	0.1024	0.252	0.0177	0.3917	-0.0902	0.0575	0.1638	-0.0823	0.0138	0.1209	-0.0018	0.0354	-0	0.153	-0.0232	-0.0749	0.1239	0.1153	0.3444	2.1712	36.6781	22.9714
36	0.2261	-0.2998	-0.1515	0.2035	0.2462	0.1632	0.0077	0.0817	0.1239	-0.0586	0.0817	0.1343	-0.0192	0.0278	-0	0.2298	-0.0621	-0.101	0.1952	0.1674	0.3389	7.1481	36.3519	16.4044
37	0.3131	-0.1559	-0.1132	0.2469	0.026	0.0314	0	-0.0455	-0.0496	0.0457	0.0184	0.2281	-0.0998	-0.0581	0	0.1347	-0.0237	0.0836	0.1402	0.0105	0.2234	-28.2039	-24.5827	61.6868
38	0.1608	-0.0839	0.1434	0.7504	-0.0143	0.0037	0.0121	-0.0175	0.006	0.0763	-0.0189	0.0516	-0.0006	-0.0149	-0	0.087	-0.025	0.0251	0.0902	0.0004	0.1127	-16.5709	-18.4903	57.5667
39	0.0618	0.0547	0.0031	0.0523	0.0436	0.0206	-0.0333	0.3658	-0.1562	-0.0528	-0.0905	0.1668	0.3411	0.2809	-0	0.1859	-0.0417	-0.0154	0.1749	-0.0335	0.2604	-13.9278	-45.5137	48.3557
40	0.1802	-0.2002	-0.2067	0.1754	0.0301	0.3525	0.0265	-0.0047	-0.0178	-0.0049	-0.0248	0.0213	0.0297	-0.0279	0	0.1123	-0.0439	-0.0152	0.1188	0.0065	0.1645	-14.9215	-32.4158	51.9859
41	0.0064	-0.0245	-0.0084	0.0052	0.0122	0.0385	0.0729	-0.1058	-0.0294	0.1829	-0.0758	0.0633	-0.1792	0.0465	0	0.3121	-0.1054	0.0623	0.3249	-0.0201	0.0934	29.0551	7.3842	96.4838
42	0.0705	0.0437	-0.059	0.182	-0.1453	0.126	0.0992	-0.2225	0.1184	0.1963	-0.0871	0.1185	-0.0545	0.011	-0	0.2474	-0.0991	0.0287	0.2688	-0.1202	0.1152	35.142	23.1085	93.9
43	0.5095	-0.1377	-0.0554	0.3687	-0.3918	0.447	-0.0006	0.0159	0.1402	0.0126	0.0276	0.0877	0.0036	-0.0072	0	0.164	-0.0475	0.0383	0.1331	-0.0425	0.1292	10.61	12.9013	79.4643
44	0.515	0.2678	-0.0738	0.456	0.0235	0.3152	0.0685	-0.0642	0.0293	0.0714	-0.038	-0.017	0.05	0.0449	0	0.2243	-0.0465	-0.0074	0.2044	-0.0169	0.1056	42.1204	11.9805	85.4013
45	0.2769	-0.2306	-0.2214	0.3269	-0.1324	0.1596	-0.0462	-0.0565	0.0821	0.093	0.0613	-0.1278	0.0593	0.081	-0	0.0899	-0.0312	-0.0327	0.0942	-0.0245	0.1356	58.9775	22.1826	62.4388
46	0.2516	-0.1919	-0.173	0.2676	0.0139	0.1804	-0.0277	-0.001	0.0043	0.0555	0.024	0.0431	0.0526	0.0368	0	0.1302	-0.0213	-0.0128	0.113	0.0089	0.1164	52.7896	4.8703	55.7614
47	0.242	-0.2724	0.0193	0.1326	0.0965	0.0903	0.0095	0.0302	0.1251	0.0665	0.0399	-0.0856	0.0589	-0.0062	0	0.1554	-0.052	0.0063	0.1293	-0.0143	0.2028	56.5613	33.3392	62.1
48	0.4928	-0.0367	0.0839	0.4262	-0.0735	0.2844	0.0379	-0.0041	0.104	-0.0589	-0.0384	0.0435	-0.0426	-0.0055	-0	0.0969	-0.0337	0.0028	0.0643	0.0235	0.1762	47.8199	34.9454	50.3325

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:89)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 90:135)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 136:317)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 318:331)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 332:405)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 406:467)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 468:524)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 525:662)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 663:737)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 738:798)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 799:881)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 882:993)
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID 994:1084)
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 1085:1210)
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 1211:1307)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 1308:1324)
17	X-RAY DIFFRACTION	17	(CHAIN E AND RESID 1325:1410)
18	X-RAY DIFFRACTION	18	(CHAIN E AND RESID 1411:1477)
19	X-RAY DIFFRACTION	19	(CHAIN E AND RESID 1478:1638)
20	X-RAY DIFFRACTION	20	(CHAIN E AND RESID 1639:1655)
21	X-RAY DIFFRACTION	21	(CHAIN F AND RESID 1657:1728)
22	X-RAY DIFFRACTION	22	(CHAIN F AND RESID 1729:1802)
23	X-RAY DIFFRACTION	23	(CHAIN F AND RESID 1803:1913)
24	X-RAY DIFFRACTION	24	(CHAIN F AND RESID 1914:1986)
25	X-RAY DIFFRACTION	25	(CHAIN G AND RESID 1987:2026)
26	X-RAY DIFFRACTION	26	(CHAIN G AND RESID 2027:2204)
27	X-RAY DIFFRACTION	27	(CHAIN G AND RESID 2205:2283)
28	X-RAY DIFFRACTION	28	(CHAIN G AND RESID 2284:2317)
29	X-RAY DIFFRACTION	29	(CHAIN H AND RESID 2318:2390)
30	X-RAY DIFFRACTION	30	(CHAIN H AND RESID 2391:2454)
31	X-RAY DIFFRACTION	31	(CHAIN H AND RESID 2455:2633)
32	X-RAY DIFFRACTION	32	(CHAIN H AND RESID 2634:2648)
33	X-RAY DIFFRACTION	33	(CHAIN I AND RESID 2649:2711)
34	X-RAY DIFFRACTION	34	(CHAIN I AND RESID 2712:2795)
35	X-RAY DIFFRACTION	35	(CHAIN I AND RESID 2796:2906)
36	X-RAY DIFFRACTION	36	(CHAIN I AND RESID 2907:2979)
37	X-RAY DIFFRACTION	37	(CHAIN J AND RESID 2980:3029)
38	X-RAY DIFFRACTION	38	(CHAIN J AND RESID 3030:3237)
39	X-RAY DIFFRACTION	39	(CHAIN J AND RESID 3238:3253)
40	X-RAY DIFFRACTION	40	(CHAIN J AND RESID 3254:3310)
41	X-RAY DIFFRACTION	41	(CHAIN K AND RESID 3311:3324)
42	X-RAY DIFFRACTION	42	(CHAIN K AND RESID 3325:3373)
43	X-RAY DIFFRACTION	43	(CHAIN K AND RESID 3374:3463)
44	X-RAY DIFFRACTION	44	(CHAIN K AND RESID 3464:3641)
45	X-RAY DIFFRACTION	45	(CHAIN L AND RESID 3642:3722)
46	X-RAY DIFFRACTION	46	(CHAIN L AND RESID 3723:3812)
47	X-RAY DIFFRACTION	47	(CHAIN L AND RESID 3813:3860)
48	X-RAY DIFFRACTION	48	(CHAIN L AND RESID 3861:3972)

-
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