PDB-2jbw: Crystal Structure of the 2,6-dihydroxy-pseudo-oxynicotine Hydrolase.

ID or keywords:

Entry

Database: PDB / ID: 2jbw

Title

Crystal Structure of the 2,6-dihydroxy-pseudo-oxynicotine Hydrolase.

Components

2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE

Keywords

HYDROLASE / ALPHA/BETA HYDROLASE / META-CLEAVAGE PATHWAY / RETRO- FRIEDEL- CRAFTS ACYLATION / NICOTINE DEGRADATION / HYPOTHETICAL PROTEIN / PLASMID / CATALYTIC TRIAD / C-C BOND CLEAVAGE

Function / homology

Function and homology information

2,6-dihydroxypseudooxynicotine hydrolase / nicotine catabolic process / alkaloid metabolic process / hydrolase activity
Similarity search - Function

Biological species

ARTHROBACTER NICOTINOVORANS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.1 Å

Authors

Schleberger, C. / Sachelaru, P. / Brandsch, R. / Schulz, G.E.

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: Structure and Action of a Cc Bond Cleaving Alpha/Beta-Hydrolase Involved in Nicotine Degration.
Authors: Schleberger, C. / Sachelaru, P. / Brandsch, R. / Schulz, G.E.

History

Deposition	Dec 14, 2006	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 4, 2007	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 / Derived calculations ...Data collection / Derived calculations / 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 / pdbx_seq_map_depositor_info / struct_conn Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn 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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2jbw.cif.gz	454.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2jbw.ent.gz	378.4 KB	Display	PDB format
PDBx/mmJSON format	2jbw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2jbw_validation.pdf.gz	459.5 KB	Display	wwPDB validaton report
Full document	2jbw_full_validation.pdf.gz	484.3 KB	Display
Data in XML	2jbw_validation.xml.gz	72.3 KB	Display
Data in CIF	2jbw_validation.cif.gz	97.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jb/2jbw ftp://data.pdbj.org/pub/pdb/validation_reports/jb/2jbw	HTTPS FTP

-
Related structure data

Similar structure data	3zuy-1 5g0x-d 3s4t-3 3s4t-2 3vxd-6 5d1d-d 3zux-1 2b81-1 5upo-d 4qa0-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE

B: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE

C: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE

D: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE

hetero molecules

176 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE

B: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE

hetero molecules

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

2

C: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE

D: 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	90.570, 57.020, 152.697
Angle α, β, γ (deg.)	90.00, 103.35, 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
1	2	A
2	2	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	139 - 384
2	1	1	5	B	139 - 384
1	1	2	5	A	40 - 111
2	1	2	5	B	40 - 111

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.421495, 0.102558, -0.901013), (0.109886, -0.992039, -0.061514), (-0.900149, -0.073081, -0.429409)	157.0857, 48.1957, 253.293
2	given	(0.580614, 0.013364, -0.814069), (0.005988, -0.999908, -0.012143), (-0.814157, 0.002176, -0.580641)	63.8634, 50.7271, 124.8256

#1: Protein	2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE / DHPON-HYDROLASE Mass: 43861.480 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-365 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARTHROBACTER NICOTINOVORANS (bacteria) / Plasmid: PH6EX3.DHPONH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q93NG6, EC: 3.7.1.-
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 964 / 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: 2.3 Å³/Da / Density % sol: 46 %
Crystal grow	Method: vapor diffusion, hanging drop / pH: 8.8 Details: PROTEINSOLUTION: 50 MM TRIS-HCL PH 7.4, 200 MM NACL, 0.5 M TCEP RESERVOIR: 35% PEG 10000, O.1 M TRIS-HCL PH 8.8 HANGING DROP, MIXED 1:1, MICROSEEDING

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 2.1→35 Å / Num. obs: 172409 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / B_iso Wilson estimate: 33.2 Å² / R_merge(I) obs: 0.05 / Net I/σ(I): 11.5
Reflection shell	Resolution: 2.09→2.16 Å / R_merge(I) obs: 0.25 / Mean I/σ(I) obs: 3.3 / % possible all: 98

-
Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
SHELXD		phasing
SHARP		phasing
REFMAC	5.2.0005	refinement

Refinement

Method to determine structure:

MAD / Resolution: 2.1→30 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.921 / SU B: 5.26 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.238	2580	2.9 %	RANDOM
R_work	0.181	-	-	-
obs	0.183	86393	99.9 %	-

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: 37.89 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.53 Å²	0 Å²	-1.63 Å²
2-	-	0.18 Å²	0 Å²
3-	-	-	-0.4 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11242	0	4	964	12210

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	11517
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.527	1.969	15652
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.919	5	1425
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.24	24.133	525
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.836	15	1927
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.916	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	1699
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	8820
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	5855
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.303	0.2	7767
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	1068
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	0.182	0.2	73
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.16	0.2	17
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	0.754	1.5	7116
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.333	2	11417
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.405	3	4637
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.328	4.5	4235
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

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Number	Type	Rms dev position (Å)	Weight position
1	904	medium positional	0.16	0.5
2	288	medium positional	0.1	0.5
1	850	loose positional	0.46	5
2	302	loose positional	0.45	5
1	904	medium thermal	1.4	2
2	288	medium thermal	0.73	2
1	850	loose thermal	2.12	10
2	302	loose thermal	1.44	10

LS refinement shell

Resolution: 2.1→2.15 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.265	186
R_work	0.208	6256

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	2.0628	-0.3222	2.6548	3.7311	1.9958	4.3453	0.0268	0.091	-0.0464	-0.2393	-0.062	-0.5312	-0.2023	0.1388	0.0352	-0.0502	-0.0415	0.0084	0.0065	0.0303	-0.1287	84.752	27.2414	132.3267
2	24.3292	4.731	-3.679	19.7423	16.4392	7.861	-0.7001	0.0366	0.7685	0.2533	0.7954	-0.6688	0.5226	0.8039	-0.0953	-0.0528	-0.0485	-0.026	0.0885	0.0539	-0.1573	86.224	33.6607	125.75
3	15.3801	0.3647	-1.4259	2.906	0.15	4.8527	-0.0945	0.4224	1.2259	-0.2057	-0.0803	-0.4096	-1.1259	-0.0102	0.1748	0.17	0.0177	-0.1121	-0.1038	-0.0368	-0.186	79.2784	41.4957	133.7179
4	8.7295	-1.2168	3.6017	1.2063	-1.1064	2.9805	0.1776	-0.5142	0.1282	0.062	-0.2648	-0.1117	-0.4284	-0.4634	0.0872	0.1386	0.0908	-0.0895	0.0615	-0.1463	-0.1598	76.9604	36.0452	139.5102
5	17.1142	-2.0592	-1.3794	1.1501	-0.4021	9.7074	-0.0879	-0.1882	1.6104	-0.1018	-0.1291	-0.3698	-1.1102	0.5859	0.217	0.1222	-0.0284	-0.1114	-0.0627	-0.0953	-0.1088	83.6863	39.9627	146.0872
6	2.2272	-0.2232	1.3444	2.7884	-0.617	9.6638	-0.0246	-0.6747	0.1841	0.4501	-0.2518	0.2771	-0.8848	-1.3492	0.2764	-0.0797	0.0927	0.0235	0.2098	-0.1734	-0.2291	69.6351	33.6623	152.5738
7	1.5496	-1.4441	1.1086	3.3327	1.2403	4.0338	-0.053	-0.4549	0.0092	0.3697	-0.1128	0.3949	0.2657	-1.0078	0.1658	-0.0569	-0.1013	0.0899	0.339	-0.0126	-0.2601	70.2872	24.504	152.6217
8	3.0923	2.3216	2.282	3.472	2.098	3.9869	-0.0893	-0.3601	-0.0571	0.2275	-0.0627	0.2354	0.0513	-0.6867	0.152	-0.0387	-0.0134	0.055	0.1983	-0.0066	-0.2278	72.8052	23.9128	147.4054
9	1.0498	-0.9013	-0.142	1.3484	1.6469	1.524	-0.1923	-0.6439	-0.0084	0.6948	-0.0488	0.0418	0.1263	-0.6001	0.2411	0.0736	-0.0442	0.0481	0.3617	0.0041	-0.3438	77.1445	25.0766	160.5712
10	4.787	1.4285	-1.0557	1.1727	2.6321	1.9946	-0.0858	-0.7077	-0.3401	0.539	-0.0097	-0.15	0.9164	-0.6536	0.0955	0.1115	-0.1703	0.0204	0.1631	0.1235	-0.2928	78.2425	14.9043	155.9425
11	3.704	0.5265	0.717	2.4818	0.6221	3.9016	-0.0359	-0.1994	-0.045	0.3256	0.1996	-0.6722	0.1344	0.4081	-0.1637	-0.04	0.0174	-0.1188	-0.0551	-0.0094	-0.089	96.4881	22.5207	149.2701
12	2.9063	-0.067	2.3491	2.5805	1.052	4.9452	0.2131	-0.3664	-0.3045	0.5735	0.1293	-0.3164	0.9062	0.0127	-0.3423	0.1166	0.0294	-0.0838	-0.0495	0.0831	-0.2133	88.8449	11.1438	151.879
13	3.5908	-1.4705	2.3935	3.3322	-2.1275	5.5298	0.311	-0.2742	-0.6396	0.3372	-0.0814	-0.1232	1.0084	-0.2103	-0.2297	0.1394	-0.0781	-0.0561	-0.1078	0.0975	-0.1553	83.9705	7.0061	144.5282
14	9.6956	4.8333	-3.2579	5.0748	-4.2781	11.2777	0.2279	-0.1155	-0.7705	0.3597	-0.2156	0.0502	0.8865	-0.673	-0.0123	0.0144	-0.1931	0.057	0.0492	0.0793	-0.178	70.9594	10.5045	143.4769
15	51.2325	-18.6466	-17.6795	14.5749	5.8692	9.0092	-1.0619	-1.9183	-2.3055	0.6002	0.7554	0.3855	1.2957	0.0936	0.3066	0.2516	-0.3034	-0.1485	-0.3287	0.0828	-0.1036	77.476	0.211	144.9677
16	3.1838	1.8041	5.0378	2.0808	0.1324	5.3872	0.0111	0.319	0.1072	-0.0415	-0.0686	-0.1627	-0.0051	0.6141	0.0575	-0.1134	0.0709	0.0269	0.0582	-0.0304	-0.0838	76.5553	22.7097	117.3385
17	7.5428	2.6637	0.6896	2.9476	0.6571	3.82	0.0138	0.1782	-0.1783	-0.3058	0.1085	-0.1717	0.9392	0.4693	-0.1223	-0.011	0.067	-0.0513	-0.0228	-0.0969	-0.0694	77.8648	10.3788	119.0301
18	-3.284	11.1727	-1.7515	20.6794	4.1487	32.9756	0.5785	-0.2887	-0.3047	-0.1221	0.3293	1.0834	2.0331	-0.65	-0.9078	0.0186	-0.28	0.028	0.0788	0.0433	-0.1412	64.7786	4.8101	135.9422
19	1.8039	0.636	0.2805	1.3206	-2.9766	12.7344	0.2046	-0.0139	-0.2095	-0.1161	-0.1972	0.0811	0.6344	-0.4818	-0.0074	-0.0179	-0.0774	-0.0301	0.0119	-0.0836	-0.095	68.575	13.6844	117.4541
20	1.9259	0.1586	-2.9327	4.2988	0.9388	16.3563	0.1301	-0.0512	-0.6408	0.1497	-0.1785	-0.0039	1.7634	-0.8002	0.0484	-0.0626	-0.185	-0.0532	0.0616	-0.0441	-0.1054	62.2834	9.1374	117.6898
21	8.3874	-1.5935	12.3867	5.3886	-2.9248	31.9881	0.1937	-0.9989	-0.9023	0.2045	-0.1967	0.4905	1.1346	-2.2785	0.003	-0.3766	-0.174	0.1751	0.6868	-0.0871	-0.2178	49.5768	14.9102	122.994
22	2.8604	0.6847	-0.5923	8.1453	4.6258	15.2395	0.0362	-0.7206	-0.0132	0.4761	-0.5085	0.8129	0.5342	-1.74	0.4722	-0.3935	-0.108	0.0818	0.6453	-0.1066	-0.1324	48.5459	19.1857	123.4101
23	2.1594	-1.0237	-0.1097	2.1886	-0.0103	4.4517	0.057	-0.364	-0.1104	0.2031	-0.38	0.0767	-0.0546	-0.846	0.323	-0.194	0.0197	0.0155	0.3236	-0.1056	-0.1582	58.0178	23.7433	120.5573
24	2.8281	-1.307	1.1277	3.0476	3.1592	7.1457	-0.0188	-0.526	-0.176	0.2297	-0.2582	0.4669	0.1641	-1.143	0.277	-0.1931	0.0027	0.0799	0.3088	-0.0609	-0.1724	55.3877	23.5874	121.9382
25	1.1618	-0.5352	-1.344	2.7795	0.6611	7.1906	0.1275	-0.5111	-0.2617	-0.1405	-0.1732	0.5935	0.3219	-1.5172	0.0457	-0.2808	0.0373	-0.0627	0.4832	-0.1513	-0.0997	48.2497	21.3882	110.3458
26	-0.9716	0.8726	0.1667	3.0813	-1.0296	5.1189	0.2424	-0.4858	-0.1248	0.2474	-0.2658	0.5582	-0.176	-0.9715	0.0234	-0.1985	0.1809	0.0223	0.4814	-0.1587	-0.1625	49.9321	29.5449	120.3021
27	4.4774	-0.5446	0.5644	1.052	-1.8486	3.061	0.0018	-0.5102	0.1979	-0.1122	-0.0401	0.3029	-0.4701	-0.8709	0.0383	-0.0865	0.285	-0.0608	0.2395	-0.2509	-0.1422	52.9937	33.92	111.8985
28	1.4686	-0.0602	1.3025	1.4666	1.0861	3.7584	-0.2334	0.0494	0.1335	-0.1527	-0.0225	0.0692	-0.5602	-0.0953	0.2559	-0.0439	0.1507	-0.0554	0.0131	-0.0993	-0.1456	62.4111	32.512	103.3612
29	1.3197	0.4173	1.5565	0.5227	-1.495	3.4226	-0.4074	-0.4328	0.4879	0.1674	-0.0238	-0.1422	-1.0468	-0.4799	0.4313	0.0895	0.2654	-0.0851	0.1323	-0.213	-0.1103	61.2089	39.4149	120.3773
30	44.0339	13.3557	-35.8968	8.9936	-14.5303	33.6313	-0.595	-0.0238	2.2368	0.2575	0.6834	0.8967	-0.868	-1.7511	-0.0885	0.3768	0.3995	-0.1536	-0.0434	-0.3919	-0.2318	59.113	47.792	120.904

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	8 - 28
2	X-RAY DIFFRACTION	2	A	29 - 35
3	X-RAY DIFFRACTION	3	A	36 - 60
4	X-RAY DIFFRACTION	4	A	61 - 89
5	X-RAY DIFFRACTION	5	A	90 - 100
6	X-RAY DIFFRACTION	6	A	101 - 122
7	X-RAY DIFFRACTION	7	A	123 - 149
8	X-RAY DIFFRACTION	8	A	150 - 176
9	X-RAY DIFFRACTION	9	A	177 - 208
10	X-RAY DIFFRACTION	10	A	209 - 237
11	X-RAY DIFFRACTION	11	A	238 - 272
12	X-RAY DIFFRACTION	12	A	273 - 306
13	X-RAY DIFFRACTION	13	A	307 - 336
14	X-RAY DIFFRACTION	14	A	337 - 350
15	X-RAY DIFFRACTION	15	A	351 - 366
16	X-RAY DIFFRACTION	16	B	6 - 28
17	X-RAY DIFFRACTION	17	B	29 - 55
18	X-RAY DIFFRACTION	18	B	56 - 66
19	X-RAY DIFFRACTION	19	B	67 - 89
20	X-RAY DIFFRACTION	20	B	90 - 108
21	X-RAY DIFFRACTION	21	B	109 - 120
22	X-RAY DIFFRACTION	22	B	121 - 137
23	X-RAY DIFFRACTION	23	B	138 - 158
24	X-RAY DIFFRACTION	24	B	159 - 178
25	X-RAY DIFFRACTION	25	B	179 - 203
26	X-RAY DIFFRACTION	26	B	204 - 221
27	X-RAY DIFFRACTION	27	B	222 - 245
28	X-RAY DIFFRACTION	28	B	246 - 309
29	X-RAY DIFFRACTION	29	B	310 - 351
30	X-RAY DIFFRACTION	30	B	352 - 365

-
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