PDB-5ve2: Crystal structure of enoyl-CoA hydratase/isomerase from Pseudoalt...

ID or keywords:

Entry

Database: PDB / ID: 5ve2

Title

Crystal structure of enoyl-CoA hydratase/isomerase from Pseudoalteromonas atlantica T6c at 2.3 A resolution.

Components

Enoyl-CoA hydratase

Keywords

ISOMERASE / LYASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC

Function / homology

Function and homology information

enoyl-CoA hydratase / enoyl-CoA hydratase activity
Similarity search - Function

Biological species

Pseudoalteromonas atlantica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Siuda, M.K. / Shabalin, I.G. / Cooper, D.R. / Chapman, H.C. / Tkaczuk, K.L. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal structure of enoyl-CoA hydratase/isomerase from Pseudoalteromonas atlantica T6c at 2.3 A resolution.
Authors: Siuda, M.K. / Shabalin, I.G. / Cooper, D.R. / Almo, S.C. / Minor, W.

History

Deposition	Apr 3, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 19, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ve2.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb5ve2.ent.gz	999.5 KB	Display	PDB format
PDBx/mmJSON format	5ve2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5ve2_validation.pdf.gz	427.5 KB	Display	wwPDB validaton report
Full document	5ve2_full_validation.pdf.gz	444.9 KB	Display
Data in XML	5ve2_validation.xml.gz	125.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ve/5ve2 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/5ve2	HTTPS FTP

-
Related structure data

Similar structure data	6ldz-1 3hrx-1 2vx2-2 3r9s-d 2vx2-1 3trr-2 2vx2-3 3trr-1 4wcz-1 5du8-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) 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
Other databases	TargetTrack: NYSGRC-028293

Similar structure data

Other databases

TargetTrack: NYSGRC-028293

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Enoyl-CoA hydratase

B: Enoyl-CoA hydratase

C: Enoyl-CoA hydratase

D: Enoyl-CoA hydratase

E: Enoyl-CoA hydratase

F: Enoyl-CoA hydratase

G: Enoyl-CoA hydratase

H: Enoyl-CoA hydratase

I: Enoyl-CoA hydratase

J: Enoyl-CoA hydratase

K: Enoyl-CoA hydratase

L: Enoyl-CoA hydratase

hetero molecules

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

1

A: Enoyl-CoA hydratase

C: Enoyl-CoA hydratase

E: Enoyl-CoA hydratase

hetero molecules

defined by author&software
Evidence: homology
91.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Enoyl-CoA hydratase

D: Enoyl-CoA hydratase

F: Enoyl-CoA hydratase

hetero molecules

defined by author&software
91.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Enoyl-CoA hydratase

I: Enoyl-CoA hydratase

K: Enoyl-CoA hydratase

hetero molecules

defined by author&software
91.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

H: Enoyl-CoA hydratase

J: Enoyl-CoA hydratase

L: Enoyl-CoA hydratase

hetero molecules

defined by author&software
91.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.660, 160.141, 136.271
Angle α, β, γ (deg.)	90.000, 90.120, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	3 - 253
2	1	B	3 - 253
1	2	A	3 - 253
2	2	C	3 - 253
1	3	A	3 - 253
2	3	D	3 - 253
1	4	A	3 - 253
2	4	E	3 - 253
1	5	A	3 - 253
2	5	F	3 - 253
1	6	A	3 - 253
2	6	G	3 - 253
1	7	A	3 - 253
2	7	H	3 - 253
1	8	A	3 - 253
2	8	I	3 - 253
1	9	A	3 - 253
2	9	J	3 - 253
1	10	A	3 - 253
2	10	K	3 - 253
1	11	A	3 - 253
2	11	L	3 - 253
1	12	B	3 - 253
2	12	C	3 - 253
1	13	B	3 - 253
2	13	D	3 - 253
1	14	B	3 - 253
2	14	E	3 - 253
1	15	B	3 - 253
2	15	F	3 - 253
1	16	B	3 - 253
2	16	G	3 - 253
1	17	B	3 - 253
2	17	H	3 - 253
1	18	B	3 - 253
2	18	I	3 - 253
1	19	B	3 - 253
2	19	J	3 - 253
1	20	B	3 - 253
2	20	K	3 - 253
1	21	B	3 - 253
2	21	L	3 - 253
1	22	C	3 - 253
2	22	D	3 - 253
1	23	C	3 - 253
2	23	E	3 - 253
1	24	C	3 - 253
2	24	F	3 - 253
1	25	C	3 - 253
2	25	G	3 - 253
1	26	C	3 - 253
2	26	H	3 - 253
1	27	C	3 - 253
2	27	I	3 - 253
1	28	C	3 - 253
2	28	J	3 - 253
1	29	C	3 - 253
2	29	K	3 - 253
1	30	C	3 - 253
2	30	L	3 - 253
1	31	D	3 - 253
2	31	E	3 - 253
1	32	D	3 - 253
2	32	F	3 - 253
1	33	D	3 - 253
2	33	G	3 - 253
1	34	D	3 - 253
2	34	H	3 - 253
1	35	D	3 - 253
2	35	I	3 - 253
1	36	D	3 - 253
2	36	J	3 - 253
1	37	D	3 - 253
2	37	K	3 - 253
1	38	D	3 - 253
2	38	L	3 - 253
1	39	E	3 - 253
2	39	F	3 - 253
1	40	E	3 - 253
2	40	G	3 - 253
1	41	E	3 - 253
2	41	H	3 - 253
1	42	E	3 - 253
2	42	I	3 - 253
1	43	E	3 - 253
2	43	J	3 - 253
1	44	E	3 - 253
2	44	K	3 - 253
1	45	E	3 - 253
2	45	L	3 - 253
1	46	F	3 - 253
2	46	G	3 - 253
1	47	F	3 - 253
2	47	H	3 - 253
1	48	F	3 - 253
2	48	I	3 - 253
1	49	F	3 - 253
2	49	J	3 - 253
1	50	F	3 - 253
2	50	K	3 - 253
1	51	F	3 - 253
2	51	L	3 - 253
1	52	G	3 - 253
2	52	H	3 - 253
1	53	G	3 - 253
2	53	I	3 - 253
1	54	G	3 - 253
2	54	J	3 - 253
1	55	G	3 - 253
2	55	K	3 - 253
1	56	G	3 - 253
2	56	L	3 - 253
1	57	H	3 - 253
2	57	I	3 - 253
1	58	H	3 - 253
2	58	J	3 - 253
1	59	H	3 - 253
2	59	K	3 - 253
1	60	H	3 - 253
2	60	L	3 - 253
1	61	I	3 - 253
2	61	J	3 - 253
1	62	I	3 - 253
2	62	K	3 - 253
1	63	I	3 - 253
2	63	L	3 - 253
1	64	J	3 - 253
2	64	K	3 - 253
1	65	J	3 - 253
2	65	L	3 - 253
1	66	K	3 - 253
2	66	L	3 - 253

NCS ensembles :

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein	Enoyl-CoA hydratase Mass: 30310.516 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas atlantica (strain T6c / ATCC BAA-1087) (bacteria) Strain: T6c / ATCC BAA-1087 / Gene: Patl_1462 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q15VV3, enoyl-CoA hydratase

#1: Protein

Enoyl-CoA hydratase

Mass: 30310.516 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudoalteromonas atlantica (strain T6c / ATCC BAA-1087) (bacteria)
Strain: T6c / ATCC BAA-1087 / Gene: Patl_1462 / Plasmid: pSGC-His / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q15VV3, enoyl-CoA hydratase

-
Non-polymers , 5 types, 2016 molecules

#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1998 / 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: 2.38 Å³/Da / Density % sol: 48.36 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 ul of 20 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the JCSG+ condition #89 (0.2M ammonium acetate, 0.1M ...Details: 0.2 ul of 20 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the JCSG+ condition #89 (0.2M ammonium acetate, 0.1M Bis-Tris pH 5.5, 45% (v/v) MPD) and equilibrated against 0.9 M NaCl solution in 96 Well 3 drop Crystallization Plate (SwissCi).

Crystal

Density Matthews: 2.38 Å³/Da / Density % sol: 48.36 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 ul of 20 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the JCSG+ condition #89 (0.2M ammonium acetate, 0.1M ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.987 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2013 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.987 Å / Relative weight: 1

Reflection

Resolution: 2.3→38 Å / Num. obs: 142189 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 3 % / B_iso Wilson estimate: 37.7 Å² / R_merge(I) obs: 0.084 / R_pim(I) all: 0.059 / R_rim(I) all: 0.103 / R_sym value: 0.084 / Χ²: 1.256 / Net I/av σ(I): 16.4 / Net I/σ(I): 6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	R_sym value	Χ²	% possible all
2.3-2.34	3.1	0.336	3.3	7281	0.933	0.23	0.409	0.336	0.803	97.5
2.34-2.38	3.1	0.298			0.942	0.204	0.362		0.833	97.5
2.38-2.43	3.1	0.285			0.952	0.195	0.347		0.834	98.2
2.43-2.48	3.1	0.245			0.946	0.168	0.298		0.871	97.7
2.48-2.53	3.1	0.227			0.966	0.156	0.276		0.861	97.9
2.53-2.59	3.1	0.201			0.969	0.138	0.244		0.892	98.3
2.59-2.66	3.1	0.188			0.974	0.129	0.229		0.941	98.1
2.66-2.73	3.1	0.17			0.977	0.117	0.207		0.969	97.9
2.73-2.81	3.1	0.145			0.982	0.099	0.176		1.035	98.1
2.81-2.9	3.1	0.133			0.985	0.091	0.162		1.136	98.1
2.9-3	3.1	0.12			0.988	0.082	0.146		1.203	98
3-3.12	3.1	0.1			0.991	0.069	0.121		1.288	96.9
3.12-3.26	3	0.084			0.992	0.058	0.103		1.274	96.8
3.26-3.44	3	0.073			0.994	0.051	0.089		1.363	95.5
3.44-3.65	2.8	0.069			0.994	0.049	0.085		1.454	87.1
3.65-3.93	2.8	0.062			0.994	0.044	0.077		1.727	70.6
3.93-4.33	2.9	0.054			0.995	0.039	0.067		1.679	94.5
4.33-4.95	2.9	0.05			0.996	0.035	0.062		1.734	95.6
4.95-6.23	3	0.055			0.996	0.038	0.067		1.81	97.7
6.23-38	2.9	0.055			0.988	0.039	0.067		3.01	93.2

-
Processing

Software

Name	Version	Classification
MD2	software from EMBL (with LS-CAT developed extensions)	data collection
HKL-3000		data scaling
SHELXD		phasing
DM		phasing
MLPHARE		phasing
HKL-3000		phasing
BUCCANEER		model building
REFMAC	5.8.0158	refinement
HKL-3000		data reduction
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.3→38 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.935 / SU B: 14.559 / SU ML: 0.187 / SU R Cruickshank DPI: 0.3991 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.399 / ESU R Free: 0.261
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2576	7178	5 %	RANDOM
R_work	0.2051	-	-	-
obs	0.2079	134973	95.14 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 281.22 Å² / B_iso mean: 47.067 Å² / B_iso min: 16.26 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.59 Å²	0 Å²	-0.05 Å²
2-	-	1.25 Å²	0 Å²
3-	-	-	1.34 Å²

Refinement step

Cycle: final / Resolution: 2.3→38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22496	0	67	1998	24561
B_iso mean	-	-	57.9	45.73	-
Num. residues	-	-	-	-	3009

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	22933
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	21795
X-RAY DIFFRACTION	r_angle_refined_deg	1.436	1.978	31066
X-RAY DIFFRACTION	r_angle_other_deg	0.96	3	50147
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.345	5	2996
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.677	24.396	960
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.211	15	3606
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.907	15	164
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	3736
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	25785
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4427

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	15600	0
1	2	B	15600	0
2	1	A	15544	0.03
2	2	C	15544	0.03
3	1	A	15492	0.03
3	2	D	15492	0.03
4	1	A	15498	0.02
4	2	E	15498	0.02
5	1	A	15488	0.02
5	2	F	15488	0.02
6	1	A	15524	0.03
6	2	G	15524	0.03
7	1	A	15562	0.02
7	2	H	15562	0.02
8	1	A	15342	0.02
8	2	I	15342	0.02
9	1	A	15570	0.02
9	2	J	15570	0.02
10	1	A	15472	0.02
10	2	K	15472	0.02
11	1	A	15524	0.02
11	2	L	15524	0.02
12	1	B	15522	0.03
12	2	C	15522	0.03
13	1	B	15484	0.03
13	2	D	15484	0.03
14	1	B	15474	0.02
14	2	E	15474	0.02
15	1	B	15492	0.02
15	2	F	15492	0.02
16	1	B	15516	0.03
16	2	G	15516	0.03
17	1	B	15528	0.02
17	2	H	15528	0.02
18	1	B	15366	0.02
18	2	I	15366	0.02
19	1	B	15546	0.02
19	2	J	15546	0.02
20	1	B	15534	0.02
20	2	K	15534	0.02
21	1	B	15496	0.02
21	2	L	15496	0.02
22	1	C	15690	0.02
22	2	D	15690	0.02
23	1	C	15566	0.02
23	2	E	15566	0.02
24	1	C	15564	0.03
24	2	F	15564	0.03
25	1	C	15588	0.03
25	2	G	15588	0.03
26	1	C	15660	0.03
26	2	H	15660	0.03
27	1	C	15362	0.04
27	2	I	15362	0.04
28	1	C	15648	0.03
28	2	J	15648	0.03
29	1	C	15480	0.03
29	2	K	15480	0.03
30	1	C	15578	0.04
30	2	L	15578	0.04
31	1	D	15504	0.03
31	2	E	15504	0.03
32	1	D	15534	0.03
32	2	F	15534	0.03
33	1	D	15584	0.03
33	2	G	15584	0.03
34	1	D	15592	0.03
34	2	H	15592	0.03
35	1	D	15334	0.04
35	2	I	15334	0.04
36	1	D	15594	0.03
36	2	J	15594	0.03
37	1	D	15452	0.03
37	2	K	15452	0.03
38	1	D	15530	0.04
38	2	L	15530	0.04
39	1	E	15506	0.02
39	2	F	15506	0.02
40	1	E	15526	0.03
40	2	G	15526	0.03
41	1	E	15540	0.02
41	2	H	15540	0.02
42	1	E	15294	0.02
42	2	I	15294	0.02
43	1	E	15588	0.02
43	2	J	15588	0.02
44	1	E	15448	0.02
44	2	K	15448	0.02
45	1	E	15492	0.03
45	2	L	15492	0.03
46	1	F	15524	0.04
46	2	G	15524	0.04
47	1	F	15578	0.03
47	2	H	15578	0.03
48	1	F	15414	0.03
48	2	I	15414	0.03
49	1	F	15582	0.03
49	2	J	15582	0.03
50	1	F	15550	0.03
50	2	K	15550	0.03
51	1	F	15534	0.03
51	2	L	15534	0.03
52	1	G	15642	0.03
52	2	H	15642	0.03
53	1	G	15356	0.03
53	2	I	15356	0.03
54	1	G	15606	0.02
54	2	J	15606	0.02
55	1	G	15524	0.03
55	2	K	15524	0.03
56	1	G	15558	0.03
56	2	L	15558	0.03
57	1	H	15390	0.02
57	2	I	15390	0.02
58	1	H	15650	0.01
58	2	J	15650	0.01
59	1	H	15540	0.02
59	2	K	15540	0.02
60	1	H	15634	0.02
60	2	L	15634	0.02
61	1	I	15460	0.02
61	2	J	15460	0.02
62	1	I	15416	0.02
62	2	K	15416	0.02
63	1	I	15396	0.02
63	2	L	15396	0.02
64	1	J	15568	0.02
64	2	K	15568	0.02
65	1	J	15646	0.02
65	2	L	15646	0.02
66	1	K	15556	0.03
66	2	L	15556	0.03

LS refinement shell

Resolution: 2.3→2.36 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.29	561	-
R_work	0.245	10140	-
all	-	10701	-
obs	-	-	96.96 %

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	3.0468	-0.0449	-0.2953	2.5953	0.6945	4.319	-0.0366	0.3351	0.1248	-0.3392	-0.0654	0.3582	-0.2319	-0.3603	0.102	0.0813	0.0388	-0.0269	0.181	-0.0056	0.1929	5.952	0.953	64.413
2	0.9627	-0.0085	-0.2931	0.7516	0.2124	1.0285	-0.0295	0.0687	0.0241	-0.0736	0.0119	0.1425	-0.1216	-0.1724	0.0176	0.1211	0.0169	-0.0138	0.1189	-0.0214	0.083	20.359	1.459	64.645
3	16.6704	6.0812	11.2832	27.234	4.9766	7.7347	0.498	0.0242	-1.3542	0.0019	0.2784	-0.2429	0.3742	0.0684	-0.7764	0.3767	-0.0164	0.04	0.42	-0.0633	0.4219	21.48	-1.614	36.73
4	3.0823	-0.0787	0.0386	3.3799	1.2668	5.5628	-0.0668	0.347	0.1912	-0.4317	-0.0854	0.4015	-0.3111	-0.3227	0.1522	0.0674	0.0289	-0.0354	0.2176	-0.019	0.2135	-33.109	-4.075	-3.766
5	1.3886	-0.1263	-0.3969	1.0655	0.1909	1.082	-0.0372	0.0243	0.0317	-0.1062	-0.0127	0.1779	-0.087	-0.168	0.0498	0.1162	0.0231	-0.0202	0.1515	-0.0313	0.079	-18.692	-3.725	-2.841
6	7.4669	0.3808	4.1606	13.11	5.256	9.6777	0.1398	0.4022	-0.9481	-0.1655	-0.5946	0.3753	0.873	-0.9983	0.4548	0.3812	-0.0751	-0.0255	0.5906	-0.1662	0.3555	-17.758	-5.036	-30.764
7	3.0505	0.4004	0.544	2.7273	-0.2085	2.2791	-0.0666	0.282	0.2848	-0.0793	-0.0989	-0.4211	-0.1707	0.4265	0.1654	0.1822	-0.063	0.0593	0.2068	0.0514	0.1279	53.691	4.38	49.246
8	0.8808	-0.1226	0.5623	1.0102	-0.0867	1.7523	-0.0421	0.1292	0.0457	-0.0891	0.0109	-0.0792	0.0512	0.0884	0.0312	0.1093	-0.0124	0.0258	0.0592	0.0028	0.0291	43.617	-1.684	59.793
9	6.2033	-1.8935	1.5458	1.4846	-0.601	1.6383	-0.0507	0.0478	-0.0208	-0.1067	-0.0294	-0.0701	0.077	0.2007	0.08	0.1592	-0.0141	0.0195	0.0674	0.0147	0.1132	58.463	9.091	69.918
10	1.3011	-0.1911	0.099	1.0098	-0.0021	1.9895	-0.0613	0.213	0.1503	-0.1603	-0.0134	-0.2451	-0.1142	0.2627	0.0746	0.1447	-0.0276	0.036	0.1048	0.0212	0.0907	11.698	-2.643	-12.087
11	2.5074	-1.5968	0.671	3.5172	-0.5047	3.0325	0.0517	0.229	-0.1071	-0.3529	-0.0566	0.0621	0.2349	0.0242	0.0049	0.1244	-0.0547	-0.0013	0.0814	-0.0218	0.0257	-1.69	-9.663	-15.575
12	6.2493	-2.2641	1.8205	1.7173	-0.7054	2.1495	-0.0043	0.1045	-0.1497	-0.0956	-0.0222	-0.0557	0.0697	0.2044	0.0264	0.1634	-0.0197	0.0173	0.0483	0.0139	0.1143	19.408	4.078	1.737
13	4.7352	0.7532	-0.9009	3.0409	0.0288	3.144	0.215	-0.8181	0.1982	0.4306	-0.1765	0.2596	-0.192	-0.136	-0.0385	0.2222	-0.0085	-0.0269	0.2777	-0.0458	0.057	43.367	2.601	97.818
14	1.929	0.3337	0.1673	0.6222	-0.1348	0.7994	0.0433	-0.247	-0.0082	0.1369	-0.0248	0.0424	-0.0549	-0.079	-0.0184	0.1272	0.0134	-0.0074	0.1054	-0.012	0.024	38.982	-0.606	84.279
15	7.8363	3.6718	-4.7807	1.8429	-2.1003	4.3514	0.2615	-0.5749	-0.0961	0.3052	-0.3026	-0.0534	-0.0509	0.0515	0.0411	0.3105	-0.0059	-0.0116	0.2179	-0.0482	0.1447	22.473	7.924	91.029
16	5.7513	1.3164	-0.9237	3.4113	-0.0735	3.1929	0.1949	-0.7806	0.2755	0.502	-0.1696	0.2365	-0.2528	-0.3005	-0.0254	0.2244	0.0013	-0.0277	0.287	-0.0399	0.0521	4.59	-2.292	29.579
17	1.7866	0.2923	0.2447	0.7446	-0.1154	1.0206	0.0294	-0.2693	-0.0201	0.1327	-0.0256	0.0348	-0.0343	-0.1791	-0.0038	0.1258	0.0126	-0.0062	0.1334	-0.0154	0.0305	-0.121	-5.597	16.118
18	12.2026	5.3112	-5.1299	2.7665	-1.9823	3.805	0.3294	-1.0173	-0.2522	0.475	-0.4849	-0.0749	0.0466	-0.1433	0.1556	0.294	0.0077	-0.0069	0.39	-0.0317	0.1233	-16.63	3.19	22.716
19	1.3899	-0.2186	-0.0527	0.8852	-0.0414	2.1889	-0.028	0.2214	-0.1407	-0.1313	-0.0135	0.2374	0.107	-0.2941	0.0416	0.1365	-0.0303	-0.0207	0.139	-0.0166	0.0784	19.74	-39.908	55.992
20	2.3193	-1.3299	-0.3022	2.8574	0.3029	2.5627	0.0366	0.1931	0.1366	-0.2917	-0.0479	-0.0538	-0.2963	0.0506	0.0112	0.1259	-0.0652	0.0103	0.1132	0.0198	0.0351	32.927	-32.565	52.991
21	7.5553	-3.002	-2.9598	2.3013	1.5861	2.3771	0.0476	0.1036	-0.0137	-0.0547	-0.1484	0.2067	-0.029	-0.1889	0.1007	0.1396	-0.019	-0.0138	0.1051	-0.0209	0.1041	12.491	-46.891	69.63
22	2.0914	-0.4565	-0.3957	1.666	0.8028	2.463	-0.0743	0.2697	-0.2542	-0.1225	-0.0235	0.3131	0.1081	-0.3235	0.0979	0.1408	-0.038	-0.0372	0.1858	-0.0102	0.0788	-19.944	-45.057	-16.039
23	19.1229	-7.533	-4.8973	4.8243	-2.4604	11.7413	0.704	0.4795	0.4927	-0.4244	-0.1069	-0.0358	-0.0715	-0.3486	-0.5971	0.7164	-0.0164	0.2331	0.1381	-0.0363	0.2013	-25.575	-48.044	2.374
24	1.1505	-0.0837	-0.1959	0.6075	0.2058	0.9715	-0.0489	0.0783	-0.0759	-0.0371	-0.0235	0.1353	-0.0574	-0.0842	0.0724	0.1249	-0.0019	-0.0005	0.1004	-0.0143	0.0395	-16.008	-44.683	-4.556
25	2.4914	0.2371	-0.2932	0.8623	0.1687	1.0967	0.083	-0.5061	-0.1443	0.3299	-0.0678	-0.0574	0.0804	0.044	-0.0151	0.2056	-0.0279	-0.0002	0.1967	0.0394	0.0516	31.772	-39.111	91.123
26	3.6371	1.3168	-0.0012	3.0844	0.9021	1.2105	0.0554	-0.2286	0.3434	0.0175	-0.067	0.2487	-0.0896	-0.0966	0.0115	0.1129	0.0076	0.0219	0.1253	0.0127	0.0503	21.953	-33.302	81.265
27	11.0589	3.7144	4.0565	2.1908	1.3199	3.3074	0.2285	-1.0867	0.1466	0.3375	-0.32	-0.0034	-0.1555	-0.0148	0.0915	0.2781	-0.0194	-0.0124	0.2669	0.0326	0.1298	48.137	-45.469	90.942
28	4.7985	1.1212	0.6229	3.036	-0.086	2.7096	0.246	-0.7043	-0.2565	0.4767	-0.1754	-0.2231	0.1647	0.0526	-0.0707	0.2673	-0.0433	0.0375	0.2797	0.0472	0.0605	-12.01	-45.05	29.701
29	2.174	0.3331	0.0355	1.0003	0.2575	0.7297	0.06	-0.2011	-0.002	0.2023	-0.0297	-0.0255	0.0307	-0.0374	-0.0302	0.1246	-0.0205	0.0143	0.1041	0.0053	0.0165	-7.576	-41.966	16.131
30	7.9197	2.7151	4.547	2.0761	1.8292	4.6016	0.2693	-0.4924	-0.0919	0.3699	-0.1383	-0.0214	0.0677	0.0369	-0.1309	0.2132	-0.015	0.0192	0.1377	0.037	0.0836	8.867	-50.391	22.892
31	3.8215	-0.1271	0.2464	3.4822	-1.2156	5.0017	0.0019	0.4244	-0.2118	-0.4526	-0.0663	-0.3516	0.2943	0.3814	0.0643	0.0721	0.0232	0.0169	0.153	-0.0247	0.207	64.569	-37.989	64.536
32	1.2304	-0.0991	0.4284	1.1724	-0.0257	1.1751	-0.0121	0.1355	-0.0184	-0.0667	0.0136	-0.202	0.0689	0.0776	-0.0014	0.1025	-0.0048	0.0256	0.1244	0.0066	0.1014	50.172	-38.628	65.125
33	16.3386	6.6352	-4.0137	14.6046	1.1432	11.5716	0.06	0.4357	1.2822	-0.0705	-0.2707	-0.0005	-0.8972	0.9377	0.2107	0.4013	-0.0231	0.0459	0.3927	0.1372	0.2248	48.939	-36.59	36.931
34	3.6046	0.0101	0.5119	3.1443	-0.8327	5.0002	-0.06	0.4216	-0.0894	-0.3982	-0.0675	-0.3184	0.2769	0.364	0.1274	0.0733	0.0218	0.0162	0.1408	-0.0362	0.186	25.399	-42.652	-3.376
35	1.5759	0.0764	0.4254	1.1042	-0.3569	1.0318	-0.0268	0.1537	0.0341	-0.0345	0.0364	-0.1418	0.0832	0.0818	-0.0096	0.1042	-0.0095	0.0157	0.089	-0.0002	0.0585	11.521	-41.672	-1.189
36	1.379	0.1974	-0.5397	2.7191	-3.3884	9.3141	0.0393	0.3743	0.1199	-0.145	-0.1396	-0.1167	0.0069	0.3883	0.1002	0.1449	0.012	0.0332	0.2287	-0.0291	0.1977	9.962	-49.966	-20.7

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 76
2	X-RAY DIFFRACTION	2	A	77 - 240
3	X-RAY DIFFRACTION	3	A	241 - 253
4	X-RAY DIFFRACTION	4	B	3 - 76
5	X-RAY DIFFRACTION	5	B	77 - 236
6	X-RAY DIFFRACTION	6	B	237 - 253
7	X-RAY DIFFRACTION	7	C	3 - 88
8	X-RAY DIFFRACTION	8	C	89 - 209
9	X-RAY DIFFRACTION	9	C	210 - 253
10	X-RAY DIFFRACTION	10	D	3 - 164
11	X-RAY DIFFRACTION	11	D	165 - 209
12	X-RAY DIFFRACTION	12	D	210 - 253
13	X-RAY DIFFRACTION	13	E	3 - 77
14	X-RAY DIFFRACTION	14	E	78 - 209
15	X-RAY DIFFRACTION	15	E	210 - 253
16	X-RAY DIFFRACTION	16	F	3 - 77
17	X-RAY DIFFRACTION	17	F	78 - 209
18	X-RAY DIFFRACTION	18	F	210 - 253
19	X-RAY DIFFRACTION	19	G	3 - 163
20	X-RAY DIFFRACTION	20	G	164 - 209
21	X-RAY DIFFRACTION	21	G	210 - 253
22	X-RAY DIFFRACTION	22	H	3 - 129
23	X-RAY DIFFRACTION	23	H	130 - 137
24	X-RAY DIFFRACTION	24	H	138 - 253
25	X-RAY DIFFRACTION	25	I	3 - 164
26	X-RAY DIFFRACTION	26	I	165 - 209
27	X-RAY DIFFRACTION	27	I	210 - 253
28	X-RAY DIFFRACTION	28	J	3 - 77
29	X-RAY DIFFRACTION	29	J	78 - 209
30	X-RAY DIFFRACTION	30	J	210 - 253
31	X-RAY DIFFRACTION	31	K	3 - 75
32	X-RAY DIFFRACTION	32	K	76 - 237
33	X-RAY DIFFRACTION	33	K	238 - 253
34	X-RAY DIFFRACTION	34	L	3 - 72
35	X-RAY DIFFRACTION	35	L	73 - 213
36	X-RAY DIFFRACTION	36	L	214 - 253

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

-
Non-polymers , 5 types, 2016 molecules

-
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 , 1 types, 12 molecules ABCDEFGHIJKL

-Non-polymers , 5 types, 2016 molecules

-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 , 1 types, 12 molecules ABCDEFGHIJKL

-
Non-polymers , 5 types, 2016 molecules

-
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