PDB-4x1c: Crystal structure of 4-OT from Pseudomonas putida mt-2 with an en...

ID or keywords:

Entry

Database: PDB / ID: 4x1c

Title

Crystal structure of 4-OT from Pseudomonas putida mt-2 with an enamine adduct on the N-terminal proline at 1.7 Angstrom resolution

Components

(2-hydroxymuconate tautomerase

) x 2

Keywords

ISOMERASE / enamine formation

Function / homology

Function and homology information

xylene catabolic process /

2-hydroxymuconate tautomerase / toluene catabolic process /

isomerase activity
Similarity search - Function

Biological species

Pseudomonas putida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Thunnissen, A.M.W.H. / Poddar, H.

Funding support

1items

Citation

Journal: Chembiochem / Year: 2015
Title: Evidence for the Formation of an Enamine Species during Aldol and Michael-type Addition Reactions Promiscuously Catalyzed by 4-Oxalocrotonate Tautomerase.
Authors: Poddar, H. / Rahimi, M. / Geertsema, E.M. / Thunnissen, A.M. / Poelarends, G.J.

History

Deposition	Nov 24, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Mar 11, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 25, 2015	Group: Database references
Revision 2.0	Jan 10, 2024	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	4x1c.cif.gz	190.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4x1c.ent.gz	155.1 KB	Display	PDB format
PDBx/mmJSON format	4x1c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x1/4x1c ftp://data.pdbj.org/pub/pdb/validation_reports/x1/4x1c	HTTPS FTP

-
Related structure data

Related structure data	4x19SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4x19-2 6ghw-1 5clo-3 6fps-1 4x19-4 5cln-5 4x19-5 1bjp-2 4x19-3 2ypd-2 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

4x19SC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#130 - Oct 2010 Riboswitches similarity (1)

Deposited unit

A: 2-hydroxymuconate tautomerase

B: 2-hydroxymuconate tautomerase

C: 2-hydroxymuconate tautomerase

D: 2-hydroxymuconate tautomerase

E: 2-hydroxymuconate tautomerase

F: 2-hydroxymuconate tautomerase

G: 2-hydroxymuconate tautomerase

H: 2-hydroxymuconate tautomerase

I: 2-hydroxymuconate tautomerase

J: 2-hydroxymuconate tautomerase

K: 2-hydroxymuconate tautomerase

L: 2-hydroxymuconate tautomerase

M: 2-hydroxymuconate tautomerase

N: 2-hydroxymuconate tautomerase

O: 2-hydroxymuconate tautomerase

hetero molecules

103 kDa, 15 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 2-hydroxymuconate tautomerase

B: 2-hydroxymuconate tautomerase

C: 2-hydroxymuconate tautomerase

D: 2-hydroxymuconate tautomerase

E: 2-hydroxymuconate tautomerase

F: 2-hydroxymuconate tautomerase

hetero molecules

defined by author&software
41.4 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: 2-hydroxymuconate tautomerase

H: 2-hydroxymuconate tautomerase

I: 2-hydroxymuconate tautomerase

J: 2-hydroxymuconate tautomerase

K: 2-hydroxymuconate tautomerase

L: 2-hydroxymuconate tautomerase

defined by author&software
41 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

M: 2-hydroxymuconate tautomerase

N: 2-hydroxymuconate tautomerase

O: 2-hydroxymuconate tautomerase

M: 2-hydroxymuconate tautomerase

N: 2-hydroxymuconate tautomerase

O: 2-hydroxymuconate tautomerase

defined by author&software
41.1 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	55.288, 85.129, 170.907
Angle α, β, γ (deg.)	90.000, 96.910, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	M-105- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
3	1	chain C
4	1	chain D
5	1	chain E
6	1	chain F
7	1	chain G
8	1	chain H
9	1	chain I
10	1	chain J
11	1	chain K
12	1	chain L
13	1	chain M
14	1	chain N
15	1	chain O

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	N80	N80	SER	SER	chain A	A	A	1 - 58	1 - 58
2	N80	N80	LEU	LEU	chain B	B	B	1 - 56	1 - 56
3	PRO	PRO	SER	SER	chain C	C	C	1 - 58	1 - 58
4	N80	N80	LYS	LYS	chain D	D	D	1 - 59	1 - 59
5	N80	N80	LYS	LYS	chain E	E	E	1 - 59	1 - 59
6	N80	N80	ALA	ALA	chain F	F	F	1 - 57	1 - 57
7	PRO	PRO	ARG	ARG	chain G	G	G	1 - 61	1 - 61
8	PRO	PRO	ARG	ARG	chain H	H	H	1 - 62	1 - 62
9	N80	N80	ALA	ALA	chain I	I	I	1 - 57	1 - 57
10	N80	N80	ALA	ALA	chain J	J	J	1 - 57	1 - 57
11	PRO	PRO	ALA	ALA	chain K	K	K	1 - 57	1 - 57
12	PRO	PRO	ALA	ALA	chain L	L	L	1 - 57	1 - 57
13	N80	N80	ALA	ALA	chain M	M	M	1 - 57	1 - 57
14	N80	N80	SER	SER	chain N	N	N	1 - 58	1 - 58
15	N80	N80	SER	SER	chain O	O	O	1 - 58	1 - 58

Details

The biological unit is a hexamer. There are 2.5 hexamer or 15 chains in the asymmetric unit.

#1: Protein	2-hydroxymuconate tautomerase / / 4-oxalocrotonate tautomerase / 4-OT Mass: 6847.876 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: xylH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01468, 2-hydroxymuconate tautomerase
#2: Protein	2-hydroxymuconate tautomerase / / 4-oxalocrotonate tautomerase / 4-OT Mass: 6821.838 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: xylH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01468, 2-hydroxymuconate tautomerase
#3: Chemical	ChemComp-NCO / COBALT HEXAMMINE(III) Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH₁₈N₆
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.95 Å³/Da / Density % sol: 36.95 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Hexaamine cobalt chloride, Bis-Tris Propane, 20% PEG3350, co-crystallised with Acetaldehyde

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.987 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 22, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 1.7→46.1 Å / Num. obs: 84590 / % possible obs: 97.7 % / Redundancy: 3.2 % / R_merge(I) obs: 0.041 / Net I/σ(I): 12.5
Reflection shell	Resolution: 1.7→1.79 Å / Mean I/σ(I) obs: 2.1 / % possible all: 95.6

-
Processing

Software

Name	Version	Classification
SCALA		data scaling
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4X19

4x19

Resolution: 1.7→42.564 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.08 / Phase error: 24.21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2274	8149	5.05 %	Random selection
R_work	0.1958	153226	-	-
obs	0.1974	161375	94.37 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 112.45 Å² / B_iso mean: 45.2663 Å² / B_iso min: 15.06 Å²

Refinement step

Cycle: final / Resolution: 1.7→42.564 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6641	0	14	305	6960
B_iso mean	-	-	55.4	43.98	-
Num. residues	-	-	-	-	871

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	6770
X-RAY DIFFRACTION	f_angle_d	0.937	9107
X-RAY DIFFRACTION	f_chiral_restr	0.037	1091
X-RAY DIFFRACTION	f_plane_restr	0.003	1155
X-RAY DIFFRACTION	f_dihedral_angle_d	12.079	2597

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	5013	X-RAY DIFFRACTION	7.925	TORSIONAL
1	2	B	5013	X-RAY DIFFRACTION	7.925	TORSIONAL
1	3	C	5013	X-RAY DIFFRACTION	7.925	TORSIONAL
1	4	D	5013	X-RAY DIFFRACTION	7.925	TORSIONAL
1	5	E	5013	X-RAY DIFFRACTION	7.925	TORSIONAL
1	6	F	5013	X-RAY DIFFRACTION	7.925	TORSIONAL
1	7	G	5013	X-RAY DIFFRACTION	7.925	TORSIONAL
1	8	H	5013	X-RAY DIFFRACTION	7.925	TORSIONAL
1	9	I	5013	X-RAY DIFFRACTION	7.925	TORSIONAL
1	10	J	5013	X-RAY DIFFRACTION	7.925	TORSIONAL
1	11	K	5013	X-RAY DIFFRACTION	7.925	TORSIONAL
1	12	L	5013	X-RAY DIFFRACTION	7.925	TORSIONAL
1	13	M	5013	X-RAY DIFFRACTION	7.925	TORSIONAL
1	14	N	5013	X-RAY DIFFRACTION	7.925	TORSIONAL
1	15	O	5013	X-RAY DIFFRACTION	7.925	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6973-1.7166	0.3642	237	0.3566	4439	4676	83
1.7166-1.7368	0.3561	313	0.3269	5129	5442	95
1.7368-1.758	0.3065	280	0.3069	5114	5394	94
1.758-1.7802	0.3239	300	0.2942	4989	5289	94
1.7802-1.8036	0.3047	313	0.2848	5178	5491	95
1.8036-1.8284	0.2992	284	0.2745	5063	5347	94
1.8284-1.8545	0.2762	280	0.2589	5115	5395	95
1.8545-1.8822	0.2707	259	0.2501	5198	5457	94
1.8822-1.9116	0.2798	251	0.2388	4817	5068	91
1.9116-1.9429	0.2723	287	0.2296	5041	5328	92
1.9429-1.9764	0.2291	230	0.2177	5117	5347	95
1.9764-2.0123	0.241	273	0.2154	5164	5437	96
2.0123-2.051	0.269	247	0.2108	5232	5479	96
2.051-2.0929	0.2456	261	0.2103	5165	5426	96
2.0929-2.1384	0.2311	258	0.2012	5200	5458	95
2.1384-2.1882	0.2432	257	0.1993	5194	5451	95
2.1882-2.2429	0.2357	283	0.1987	5116	5399	95
2.2429-2.3035	0.2251	254	0.1985	5081	5335	92
2.3035-2.3713	0.2383	262	0.1909	4916	5178	93
2.3713-2.4478	0.2033	254	0.1874	5289	5543	96
2.4478-2.5353	0.2329	297	0.1976	5258	5555	96
2.5353-2.6368	0.2353	250	0.1938	5154	5404	96
2.6368-2.7568	0.2159	294	0.1936	5203	5497	97
2.7568-2.9021	0.206	251	0.1963	5246	5497	96
2.9021-3.0839	0.2713	255	0.2268	4926	5181	91
3.0839-3.3219	0.2377	259	0.1973	5329	5588	98
3.3219-3.656	0.2097	328	0.1855	5245	5573	97
3.656-4.1847	0.1659	287	0.1593	5210	5497	96
4.1847-5.2707	0.1957	273	0.1489	5029	5302	93
5.2707-42.5779	0.2481	272	0.2015	5069	5341	93

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	3.4013	-1.7281	2.8203	8.9492	-2.4823	2.0116	-0.0726	0.333	0.0739	-0.0073	-0.0071	0.1241	-0.515	-0.0168	0.0106	0.1492	0.0192	0.0109	0.2193	-0.0076	0.2234	-4.956	-1.221	-29.2144
2	7.9953	-3.4543	7.8018	7.3571	-4.227	2.0923	0.8014	1.0778	-0.4624	-0.5928	-0.5069	-0.066	1.1352	1.2333	-0.3817	0.2471	0.133	0.003	0.3474	-0.0684	0.2823	2.8539	-10.3592	-29.0472
3	8.3768	-7.0058	3.7807	2.2209	-1.8659	5.0018	0.2811	0.2086	-0.3424	-0.1593	-0.3164	-0.0304	0.3148	0.2775	-0.1867	0.1787	-0.0272	-0.0512	0.1287	0.0052	0.3379	-4.2816	-6.7118	-24.8803
4	6.4432	3.9554	5.2036	2.0034	-2.9776	8.2313	-0.2008	1.1783	0.7791	-1.9141	-0.4809	-0.13	-1.3285	0.8782	0.7018	0.5126	-0.0472	-0.0255	0.3715	0.0729	0.249	-6.308	14.7777	-28.1577
5	8.2071	3.9327	3.975	6.3908	-0.3049	8.0325	-0.0533	-0.2798	-0.3295	-0.1988	0.0857	0.46	-0.2024	-0.6335	0.0074	0.1535	0.0397	0.0248	0.154	-0.0501	0.1652	-17.4888	7.7481	-22.3243
6	2.2437	3.0101	6.467	6.7006	1.1172	2.1461	-0.8083	0.0342	0.7004	-0.4647	0.1129	0.3809	-1.1936	-0.0191	0.7517	0.3144	0.0042	-0.0654	0.2545	-0.0015	0.3124	-11.6205	18.7954	-20.5713
7	9.0533	5.3679	4.6918	2.0101	1.063	6.2488	-0.6204	0.3953	0.027	-0.7714	0.5045	-0.8846	-0.737	0.8948	0.0088	0.3483	-0.1664	0.0165	0.3282	0.0421	0.3283	-0.5381	16.8821	-18.4559
8	7.8577	7.1157	1.2581	2.0658	0.2527	6.0143	-0.1591	0.0195	0.3367	-0.151	0.1323	0.5569	0.0112	-0.6172	0.0111	0.1704	0.0296	-0.0209	0.1916	0.0258	0.4526	-18.7579	3.442	-23.5402
9	2.0011	-4.0632	1.999	7.8624	-6.5489	2.0054	0.3644	-0.6372	0.2252	0.019	-0.0363	1.6383	0.3196	-2.1548	-0.2286	0.2338	-0.0535	0.056	0.7218	-0.0126	0.3748	-28.1122	-2.1962	-14.7925
10	2.0396	3.0688	3.4932	6.245	3.7825	9.3209	-0.0505	0.1799	-0.2484	0.1423	0.3387	-0.4409	0.0664	0.4456	-0.232	0.1592	0.0325	0.0158	0.1823	0.0034	0.2521	-5.5828	8.7313	-10.0593
11	2.1343	-2.6857	1.8433	5.3716	-2.0022	2.0869	-0.6008	-0.7122	0.5111	0.0848	0.2926	0.3138	-0.995	-0.9654	0.4324	0.2821	0.1036	0.012	0.2663	-0.0306	0.2961	-13.0392	16.779	-9.2239
12	6.1433	-2.3284	-0.9961	5.4309	1.3148	6.3791	-0.1421	-0.438	0.3873	0.1049	0.2187	-0.2375	-0.1118	0.1465	-0.0654	0.1709	-0.0422	0.0057	0.0291	0.018	0.178	-4.938	7.4302	-12.9102
13	8.0916	-0.4509	2.6306	5.9301	-2.3703	8.7075	0.1356	-0.3184	-0.3642	0.2282	0.2718	0.0477	0.4988	0.0718	-0.3744	0.2014	0.0112	-0.0022	0.1418	-0.0444	0.2232	1.9461	-6.371	-12.9982
14	8.6703	-0.4092	6.2415	4.8783	-1.7489	2.0288	0.0506	1.044	0.1111	-0.1486	-0.1034	-0.6123	0.0588	1.5915	-0.0057	0.1748	0.0302	0.084	0.3271	-0.0263	0.2897	9.5784	-3.8154	-21.6819
15	8.5392	2.9318	-4.8681	5.617	-4.1298	2.1597	-0.1413	0.0943	0.1439	-0.0801	-0.1233	-0.2584	0.0086	0.1641	0.2374	0.2477	-0.0829	-0.0531	0.1769	-0.014	0.2067	1.9861	-1.4615	-18.0251
16	2.0065	2.3156	1.4942	2.0061	0.2305	8.5583	0.1753	-0.9774	-1.4284	0.6245	-0.6111	-0.5962	2.0097	0.3726	0.4667	0.5766	0.0481	0.0118	0.3786	0.1126	0.5628	-7.3377	-18.5433	-7.2424
17	3.5782	-0.9638	0.6769	5.4517	0.6362	2.0133	0.0951	-0.1983	0.0522	0.318	0.0092	-0.1033	-0.6023	-0.4402	-0.1131	0.2226	-0.0581	0.0126	0.2175	0.0108	0.258	-12.7097	-4.8546	-4.9384
18	8.9791	3.8235	8.6941	5.2016	4.3743	2.0608	0.6899	-0.2751	-0.7267	0.3561	0.0207	0.0681	1.6353	-0.8546	-0.7189	0.4628	-0.277	-0.04	0.3764	0.0903	0.3613	-17.1785	-15.705	-6.9604
19	4.924	3.2412	1.8808	2.0937	2.8039	7.6185	0.3229	0.0159	-0.4826	0.0559	-0.0798	-0.2937	0.6222	-0.2862	-0.2366	0.2727	-0.0074	-0.0283	0.1486	0.028	0.2445	-11.8567	-9.4744	-10.2235
20	8.8725	-2.8018	2.1183	9.0411	1.3362	2.0037	-0.5107	-1.4318	0.7941	2.587	-0.3467	0.4934	-0.5943	-1.3472	0.7734	0.5454	0.0508	0.1539	0.503	-0.1205	0.3632	-16.9654	10.5773	-1.9806
21	6.7304	-0.1547	1.5315	4.16	3.6238	2.0365	0.0923	0.2671	-0.0734	0.0876	0.2225	0.1428	0.3445	-0.1113	-0.305	0.2394	-0.0623	0.0222	0.2202	0.0755	0.2079	-18.0821	-8.9906	-22.0407
22	6.0811	1.3647	2.5705	3.2815	2.0679	2.0243	0.5607	-0.8572	0.0237	0.3117	-0.388	0.3684	1.4176	-2.2605	-0.1243	0.2961	-0.2675	0.0707	0.5987	0.0229	0.3316	-25.8802	-10.7796	-12.9451
23	9.2006	-0.3103	-0.5926	2.654	4.0171	6.0863	-0.0449	-0.6109	0.5453	0.7377	-0.1651	0.4771	-0.1113	-1.4084	0.0775	0.2636	0.0584	0.1357	0.7841	-0.0941	0.271	-24.8867	-2.4701	-4.8464
24	2.0728	-1.5242	-6.2154	2.8997	0.8129	2.0268	-0.205	0.4569	-0.4893	-0.1414	-0.0998	0.2163	0.6285	-0.5808	0.0622	0.1883	0.0183	-0.0124	0.5041	-0.1283	0.2726	-15.3619	-7.3209	-25.4071
25	2.0015	1.9949	0.5417	2.002	2.2005	2.0068	0.0628	1.4656	-1.5379	-0.2265	-0.6136	0.623	1.0815	-0.2141	0.5353	0.3863	0.0784	-0.0449	0.3632	-0.1392	0.3711	-4.8248	-15.5157	-28.1351
26	2.0369	1.0777	6.5685	4.2582	1.2039	2.1271	-0.2843	0.164	0.2522	0.0746	0.1048	0.0005	-0.5554	0.0222	0.1164	0.2466	-0.0629	0.0805	0.371	-0.0321	0.2402	-27.5704	8.1958	-41.7603
27	9.78	-1.5567	6.8826	4.5422	-0.6149	2.051	-0.5955	-1.352	0.621	0.3451	0.3097	0.1114	-1.0246	-1.7107	0.2806	0.3204	0.186	0.0748	0.5117	-0.029	0.2737	-37.5569	12.43	-39.6819
28	2.0102	-2.2319	3.5626	4.3809	-0.6609	5.694	0.0598	-0.3301	-0.3486	-0.012	0.225	0.6427	-0.1211	-0.8231	-0.261	0.1967	0.0099	0.0814	0.3364	0.0774	0.3064	-37.3527	5.3029	-42.7905
29	5.2195	3.3776	-1.4033	6.4846	-3.3872	8.5272	0.094	-0.0567	1.6477	0.3174	-0.6416	-0.8057	-1.514	1.7272	0.403	0.4767	-0.1807	0.0226	0.5075	0.1151	0.6414	-12.525	11.5458	-45.9744
30	9.5573	-2.104	4.569	5.9757	-2.123	8.0489	0.3172	0.2293	-0.1632	-0.0232	-0.1487	0.1285	0.5099	0.4327	-0.106	0.1986	0.0704	0.0603	0.2889	-0.0103	0.1997	-15.3603	-1.5269	-48.0381
31	4.8582	-1.1275	2.9693	4.0179	-4.0423	2.0205	0.0318	1.4852	0.811	-0.0653	-0.551	-0.3663	-0.7654	1.8476	0.4504	0.3656	0.0359	0.1366	0.8399	0.1868	0.3695	-9.1682	4.7065	-54.7929
32	3.9723	-0.3993	-2.8903	1.9958	-2.5697	6.3056	0.086	1.4511	1.0556	-0.9523	-0.476	-0.5882	-0.9601	0.5417	0.3477	0.4526	-0.1074	0.062	0.8129	0.6493	0.7053	-15.3086	12.9763	-61.2095
33	2.0613	-1.9111	1.9893	2.0151	-8.7928	2.0789	-0.0213	0.3704	0.0847	0.4643	0.0695	-0.0051	-0.6418	0.2835	-0.0013	0.4332	-0.0018	0.0654	0.2812	0.0345	0.292	-17.4972	2.0733	-47.4414
34	9.4574	3.3904	3.2159	2.0106	5.1645	2.0222	0.4117	0.42	-0.9439	-0.4149	-0.2276	-0.8683	0.9717	0.2795	-0.1794	0.5391	0.0881	0.0109	0.2591	0.0059	0.3794	-19.7193	-15.2717	-43.3797
35	2.0013	-4.7793	6.3244	2.0047	-1.6099	2.0013	-0.0076	-0.1601	-1.9135	0.2837	0.1522	-0.1543	1.6202	0.8439	-0.1585	0.7096	0.1188	-0.0509	0.4325	0.0626	0.7983	-13.4129	-18.9618	-41.6805
36	6.0784	-1.9852	1.8792	6.9437	-1.5707	2.0129	0.2475	-0.4638	-0.1587	0.1422	0.1183	-0.0958	0.1024	-0.6	-0.2924	0.1929	-0.0684	-0.0117	0.204	0.0064	0.2538	-28.9991	-8.1215	-39.7125
37	6.4497	-0.054	1.4941	6.6526	2.2085	2.0321	0.4557	-0.3771	-1.0318	-0.4365	0.3058	0.5768	1.9463	-0.0871	-0.7639	0.8879	-0.2039	-0.2826	0.0978	0.0382	0.5697	-28.8881	-19.3461	-43.4114
38	4.421	-0.7193	1.1322	9.0912	2.4351	6.2457	0.3996	0.3555	-0.358	-0.5948	0.1458	-0.1906	1.0034	0.1302	-0.4703	0.4744	0.0168	-0.0464	0.1754	-0.0143	0.2198	-26.6811	-11.3792	-46.2959
39	2.008	0.057	-1.9666	7.1752	-2.5022	2.008	-0.5197	-1.9944	-0.2989	1.5517	0.6936	0.953	0.2933	-1.101	-0.1216	0.4958	0.0931	0.038	0.7205	0.101	0.3633	-39.0388	2.6151	-34.1619
40	2.04	-0.1036	7.0393	6.5244	-0.6535	2.0813	0.5963	-0.0731	-0.2682	-0.5446	-0.0968	0.2034	0.0938	-0.4683	-0.4448	0.2977	0.0204	0.0648	0.5318	-0.0084	0.1776	-38.1928	5.2208	-54.5766
41	2.1472	1.1381	1.8916	2.1138	3.6324	2.0496	-0.6163	-0.2366	0.8814	-0.5557	-0.195	0.1766	-1.7596	-0.5661	0.8798	0.638	0.1109	-0.0525	0.3067	-0.0101	0.3229	-37.1259	16.4398	-50.9829
42	3.006	-0.7285	1.495	7.1983	0.1669	7.7738	0.0836	-0.3242	-0.3354	-0.5761	0.0199	0.1382	-0.0898	-0.5647	-0.0634	0.117	0.0286	0.0228	0.3069	0.0717	0.2215	-36.1312	3.8425	-52.1761
43	5.9686	-2.7804	2.8957	7.2352	-2.1029	9.4468	-0.2209	0.5261	0.2329	0.0665	-0.0793	-0.1533	-0.1262	0.4507	0.1946	0.2007	0.0707	0.0432	0.3495	-0.0238	0.2218	-22.847	2.2547	-61.4448
44	6.1459	-1.4733	5.4049	2.9958	-1.3307	1.9927	-0.0777	1.501	-0.0638	-0.7497	-0.0704	-0.494	0.3904	1.7719	0.2399	-0.3531	0.6462	0.8346	0.9943	-0.325	-0.2517	-13.1103	-2.1218	-64.1045
45	7.9715	-1.9645	0.5201	3.7948	1.0776	3.6065	0.6304	0.8035	-0.4457	-0.3226	-0.377	-0.0883	0.4165	0.9935	-0.1794	0.3785	0.1902	0.0724	0.4941	-0.0412	0.2441	-19.8614	-2.4528	-58.4976
46	2.0033	-1.0651	6.184	2.0022	2.5121	2.0034	0.118	0.7004	1.3507	-1.0667	-0.6658	-0.3115	-1.3548	0.4798	0.5349	0.5242	-0.0415	0.0334	0.3916	0.0271	0.4478	-30.4373	16.8567	-57.5013
47	6.7582	1.8462	3.4817	6.4297	1.1008	2.0055	0.2148	0.2785	-0.2683	-1.1807	0.4029	0.3677	1.0984	0.1064	-0.4519	0.5748	-0.0887	-0.1015	0.1779	-0.0063	0.2862	-32.8365	-10.1502	-56.2509
48	4.471	0.9622	3.422	4.9937	-0.7418	6.9841	0.4266	-0.5123	-0.25	-0.506	0.2254	0.6714	2.1134	-1.8058	-0.4856	0.8289	-0.3843	-0.2261	0.5418	0.2068	0.5379	-39.1881	-16.9269	-49.4523
49	4.9409	0.7871	2.2827	5.4043	-1.2353	3.7121	0.2972	0.1845	-0.6315	-0.7057	0.1254	0.21	1.3043	-0.1745	-0.3269	0.4219	0.0489	-0.0844	0.2314	-0.0259	0.3311	-30.4407	-9.2675	-54.9946
50	2.0441	-0.5915	7.5012	5.6723	0.8417	9.1504	0.5201	0.8062	-0.6427	0.2414	-0.0345	-0.22	0.3347	1.3264	-0.3766	0.2374	0.0098	0.0148	0.4788	-0.0163	0.2491	-32.7087	1.5634	-81.4166
51	5.4121	-1.1644	3.3198	6.9573	-3.0627	2.0079	-0.8169	1.2097	0.7552	-0.016	0.2171	-0.8051	-1.2507	1.9725	0.7313	0.4404	-0.3011	-0.0205	0.8222	0.1142	0.348	-29.5119	11.5823	-86.3862
52	3.3215	1.0401	3.6083	8.4426	-1.6086	4.8647	-0.6521	1.4071	1.1469	-0.2216	0.0643	0.2127	-1.644	0.6599	0.5252	0.6581	-0.2961	-0.2674	0.6907	0.3272	0.5373	-39.2611	17.0531	-91.6907
53	2.4878	0.2758	0.7855	8.8841	2.1569	3.2939	0.7452	-0.0392	-0.8202	0.1775	0.1618	-0.9449	1.1708	1.2843	-0.6733	0.5989	0.2495	-0.3042	0.4618	-0.0942	0.561	-33.2029	-6.6891	-80.41
54	6.6921	1.9426	2.6114	7.8458	2.6968	2.0434	-0.2518	-0.4208	0.0871	0.1882	0.3354	0.0142	-0.2769	-0.5555	-0.105	0.2661	0.04	0.0086	0.4364	0.0472	0.1572	-47.0372	6.2782	-74.1097
55	7.2484	1.7076	4.482	3.7661	2.1606	6.4947	-0.2186	-1.2217	0.1057	0.4508	0.2121	0.4005	-0.6345	-2.0328	-0.0281	0.212	0.1128	0.0391	1.2989	0.0622	0.3908	-58.4021	6.212	-72.0609
56	2.0479	2.0262	1.1232	3.8312	0.2331	4.2953	0.164	-1.0865	-0.0802	0.0146	-0.0813	0.3256	0.1319	-1.1918	-0.0993	0.2872	-0.0737	-0.0493	0.6809	0.0696	0.3053	-51.9258	1.8865	-76.0556
57	2.006	0.1255	4.5006	2.0023	-1.7741	2.0034	-0.4496	-0.2535	1.9688	0.5493	-0.1748	-0.7784	-2.2873	1.379	0.4875	0.6328	-0.1603	-0.0951	0.4944	0.0298	0.5854	-36.0798	15.8019	-79.8368
58	3.8738	-1.96	2.471	4.1702	-2.7882	2.0066	0.7189	-0.3111	-0.7669	0.339	0.2512	-0.0364	0.9596	-0.5303	-0.9289	0.7993	-0.0683	-0.3297	0.3085	0.0717	0.3853	-43.6036	-10.0212	-75.812
59	2.0523	-0.3497	0.9123	3.5041	0.6806	9.338	0.5918	0.6727	-0.9805	-0.279	0.0936	-0.3443	2.0423	0.8085	-0.7272	1.2667	0.8737	-1.315	-0.1246	0.4475	0.1462	-38.5892	-18.7226	-84.9976
60	8.1939	-4.6699	-1.3899	7.4565	3.3591	2.0084	0.1793	-0.7338	-0.4755	0.6319	0.4842	-0.0394	1.5821	-0.5152	-0.7518	0.5313	0.0036	-0.1608	0.4733	0.043	0.314	-43.9569	-5.8802	-73.7741
61	7.9878	0.2809	-3.1384	2.8111	0.5548	2.0022	-0.312	-1.5903	-0.4986	1.8234	0.4499	0.815	0.8403	-1.6263	-0.1178	0.6568	-0.1633	0.0562	1.4442	0.2574	0.5166	-56.7016	-3.4083	-69.3038

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 12 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 13 through 31 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 32 through 49 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 50 through 58 )	A
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 12 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 13 through 31 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 32 through 39 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 40 through 49 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 50 through 56 )	B
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1 through 12 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 13 through 31 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 32 through 58 )	C
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 2 through 12 )	D
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 13 through 31 )	D
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 32 through 49 )	D
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 50 through 59 )	D
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 2 through 12 )	E
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 13 through 31 )	E
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 32 through 49 )	E
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 50 through 59 )	E
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 2 through 12 )	F
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 13 through 31 )	F
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 32 through 39 )	F
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 40 through 49 )	F
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 50 through 57 )	F
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 1 through 12 )	G
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 13 through 31 )	G
28	X-RAY DIFFRACTION	28	chain 'G' and (resid 32 through 45 )	G
29	X-RAY DIFFRACTION	29	chain 'G' and (resid 46 through 61 )	G
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 1 through 12 )	H
31	X-RAY DIFFRACTION	31	chain 'H' and (resid 13 through 31 )	H
32	X-RAY DIFFRACTION	32	chain 'H' and (resid 32 through 38 )	H
33	X-RAY DIFFRACTION	33	chain 'H' and (resid 39 through 45 )	H
34	X-RAY DIFFRACTION	34	chain 'H' and (resid 46 through 56 )	H
35	X-RAY DIFFRACTION	35	chain 'H' and (resid 57 through 62 )	H
36	X-RAY DIFFRACTION	36	chain 'I' and (resid 2 through 12 )	I
37	X-RAY DIFFRACTION	37	chain 'I' and (resid 13 through 30 )	I
38	X-RAY DIFFRACTION	38	chain 'I' and (resid 31 through 49 )	I
39	X-RAY DIFFRACTION	39	chain 'I' and (resid 50 through 60 )	I
40	X-RAY DIFFRACTION	40	chain 'J' and (resid 2 through 12 )	J
41	X-RAY DIFFRACTION	41	chain 'J' and (resid 13 through 31 )	J
42	X-RAY DIFFRACTION	42	chain 'J' and (resid 32 through 57 )	J
43	X-RAY DIFFRACTION	43	chain 'K' and (resid 1 through 12 )	K
44	X-RAY DIFFRACTION	44	chain 'K' and (resid 13 through 30 )	K
45	X-RAY DIFFRACTION	45	chain 'K' and (resid 31 through 49 )	K
46	X-RAY DIFFRACTION	46	chain 'K' and (resid 50 through 57 )	K
47	X-RAY DIFFRACTION	47	chain 'L' and (resid 1 through 12 )	L
48	X-RAY DIFFRACTION	48	chain 'L' and (resid 13 through 31 )	L
49	X-RAY DIFFRACTION	49	chain 'L' and (resid 32 through 57 )	L
50	X-RAY DIFFRACTION	50	chain 'M' and (resid 2 through 12 )	M
51	X-RAY DIFFRACTION	51	chain 'M' and (resid 13 through 30 )	M
52	X-RAY DIFFRACTION	52	chain 'M' and (resid 31 through 39 )	M
53	X-RAY DIFFRACTION	53	chain 'M' and (resid 40 through 57 )	M
54	X-RAY DIFFRACTION	54	chain 'N' and (resid 2 through 12 )	N
55	X-RAY DIFFRACTION	55	chain 'N' and (resid 13 through 31 )	N
56	X-RAY DIFFRACTION	56	chain 'N' and (resid 32 through 49 )	N
57	X-RAY DIFFRACTION	57	chain 'N' and (resid 50 through 58 )	N
58	X-RAY DIFFRACTION	58	chain 'O' and (resid 2 through 12 )	O
59	X-RAY DIFFRACTION	59	chain 'O' and (resid 13 through 39 )	O
60	X-RAY DIFFRACTION	60	chain 'O' and (resid 40 through 49 )	O
61	X-RAY DIFFRACTION	61	chain 'O' and (resid 50 through 58 )	O

-
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