PDB-4jyl: Crystal structure of enoyl-CoA hydratase from Thermoplasma volcan...

ID or keywords:

Entry

Database: PDB / ID: 4jyl

Title

Crystal structure of enoyl-CoA hydratase from Thermoplasma volcanium GSS1

Components

Enoyl-CoA hydratase

Keywords

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

Function / homology

Function and homology information

catalytic activity
Similarity search - Function

Biological species

Thermoplasma volcanium (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.37 Å

Authors

Shabalin, I.G. / Cooper, D.R. / Majorek, K.A. / Mikolajczak, K. / Porebski, P.J. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Bonanno, J. / Seidel, R. ...

Citation

Journal: To be Published
Title: Crystal structure of enoyl-CoA hydratase from Thermoplasma volcanium GSS1
Authors: Shabalin, I.G. / Cooper, D.R. / Majorek, K.A. / Mikolajczak, K. / Porebski, P.J. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / New York ...

History

Deposition	Mar 29, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 17, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 13, 2022	Group: Database references / Derived calculations / Structure summary Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4jyl.cif.gz	571.7 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	4jyl.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4jyl_validation.pdf.gz	487.9 KB	Display	wwPDB validaton report
Full document	4jyl_full_validation.pdf.gz	496.9 KB	Display
Data in XML	4jyl_validation.xml.gz	56.7 KB	Display
Data in CIF	4jyl_validation.cif.gz	81.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jy/4jyl ftp://data.pdbj.org/pub/pdb/validation_reports/jy/4jyl	HTTPS FTP

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Related structure data

Similar structure data	6ojm-2 3h02-d 2hw5-d 4eml-d 4elx-d 5z7r-1 4jcs-1 4elw-d 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-028058

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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

hetero molecules

177 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	80.102, 117.229, 91.505
Angle α, β, γ (deg.)	90.000, 91.430, 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	-5 - 243
2	1	B	-5 - 243
1	2	A	-4 - 242
2	2	C	-4 - 242
1	3	A	0 - 241
2	3	D	0 - 241
1	4	A	-4 - 242
2	4	E	-4 - 242
1	5	A	1 - 241
2	5	F	1 - 241
1	6	B	-4 - 242
2	6	C	-4 - 242
1	7	B	0 - 241
2	7	D	0 - 241
1	8	B	-4 - 242
2	8	E	-4 - 242
1	9	B	1 - 241
2	9	F	1 - 241
1	10	C	0 - 241
2	10	D	0 - 241
1	11	C	-4 - 243
2	11	E	-4 - 243
1	12	C	1 - 241
2	12	F	1 - 241
1	13	D	0 - 241
2	13	E	0 - 241
1	14	D	1 - 241
2	14	F	1 - 241
1	15	E	1 - 241
2	15	F	1 - 241

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	Enoyl-CoA hydratase Mass: 29473.088 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma volcanium (archaea) / Strain: GSS1 / Gene: 1441684, TV0198 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q97CA4, enoyl-CoA hydratase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 667 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.36 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1 ul of 15.3 mg/ml protein in 20mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5mM TCEP were mixed with 1 ul of The Cryos Suite condition #26 (0.07 M tri-Sodium citrate ...Details: 1 ul of 15.3 mg/ml protein in 20mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5mM TCEP were mixed with 1 ul of The Cryos Suite condition #26 (0.07 M tri-Sodium citrate pH 5.6, 0.7 M Ammonium phosphate, 30% (v/v) Glycerol) and equilibrated against 1.9 M NaCl in QIAGEN EasyXtal 15-Well Tool plate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal

Density Matthews: 2.43 Å³/Da / Density % sol: 49.36 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1 ul of 15.3 mg/ml protein in 20mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5mM TCEP were mixed with 1 ul of The Cryos Suite condition #26 (0.07 M tri-Sodium citrate ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2013 / Details: C(111)

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.37→50 Å / Num. all: 68626 / Num. obs: 68489 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / B_iso Wilson estimate: 36.8 Å² / R_merge(I) obs: 0.165 / R_sym value: 0.165 / Χ²: 3.595 / Net I/σ(I): 15.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	R_sym value	Χ²	% possible all
2.37-2.41	3.7	0.68	1.9	3387	0.68	0.725	99.1
2.41-2.45	3.7	0.569		3390		0.743	99.4
2.45-2.5	3.7	0.503		3423		0.73	99.6
2.5-2.55	3.8	0.45		3372		0.779	99.6
2.55-2.61	3.9	0.403		3416		0.811	99.5
2.61-2.67	4	0.35		3420		0.805	99.7
2.67-2.74	4.2	0.312		3395		0.912	99.9
2.74-2.81	4.5	0.276		3401		0.997	100
2.81-2.89	4.9	0.241		3427		1.138	100
2.89-2.99	5.4	0.219		3423		1.28	100
2.99-3.09	5.7	0.189		3451		1.513	100
3.09-3.22	5.8	0.169		3384		1.761	100
3.22-3.36	5.8	0.149		3429		2.165	100
3.36-3.54	5.4	0.145		3463		2.824	100
3.54-3.76	2.8	0.388		3404		37.624	99.9
3.76-4.05	4.4	0.123		3447		5.044	99.9
4.05-4.46	5.8	0.113		3431		6.209	100
4.46-5.1	5.7	0.099		3448		5.544	99.9
5.1-6.43	5.8	0.094		3463		4.273	100
6.43-50	5.6	0.081		3515		8.02	99.9

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
HKL-3000		data collection
SHELX		phasing
MLPHARE		phasing
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.37→45.78 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.941 / WR_factor R_free: 0.1698 / WR_factor R_work: 0.1437 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9092 / SU B: 10.67 / SU ML: 0.125 / SU R Cruickshank DPI: 0.3189 / SU R_free: 0.1975 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.319 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1905	3464	5.1 %	RANDOM
R_work	0.1573	-	-	-
all	0.1589	68596	-	-
obs	0.1589	68445	99.78 %	-

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 max: 108.51 Å² / B_iso mean: 31.6749 Å² / B_iso min: 7.13 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.24 Å²	-0 Å²	1.64 Å²
2-	-	-0.47 Å²	-0 Å²
3-	-	-	1.67 Å²

Refinement step

Cycle: LAST / Resolution: 2.37→45.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11247	0	11	667	11925

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.019	11477
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	11426
X-RAY DIFFRACTION	r_angle_refined_deg	1.717	2.007	15449
X-RAY DIFFRACTION	r_angle_other_deg	1.372	3	26345
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.953	5	1492
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.022	24.774	465
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.542	15	1997
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.982	15	73
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	1759
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	12930
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	2383

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	14846	0.09
1	2	B	14846	0.09
2	1	A	14810	0.08
2	2	C	14810	0.08
3	1	A	14577	0.07
3	2	D	14577	0.07
4	1	A	14804	0.08
4	2	E	14804	0.08
5	1	A	14729	0.06
5	2	F	14729	0.06
6	1	B	14642	0.09
6	2	C	14642	0.09
7	1	B	14387	0.08
7	2	D	14387	0.08
8	1	B	14652	0.09
8	2	E	14652	0.09
9	1	B	14494	0.08
9	2	F	14494	0.08
10	1	C	14592	0.08
10	2	D	14592	0.08
11	1	C	14770	0.09
11	2	E	14770	0.09
12	1	C	14639	0.07
12	2	F	14639	0.07
13	1	D	14680	0.07
13	2	E	14680	0.07
14	1	D	14574	0.07
14	2	F	14574	0.07
15	1	E	14542	0.08
15	2	F	14542	0.08

LS refinement shell

Resolution: 2.37→2.431 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.279	255	-
R_work	0.24	4751	-
all	-	5006	-
obs	-	4751	99.13 %

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	5.1189	2.8804	-8.8666	1.6398	-4.9991	15.3982	-0.1473	-0.9142	-0.2794	-0.0828	-0.4159	-0.1168	0.3582	1.5583	0.5631	0.5259	0.1225	0.1168	0.685	0.3138	0.5324	35.062	-0.096	48.678
2	1.5683	-0.5745	-0.16	0.9138	0.071	0.8214	-0.0923	-0.2538	-0.2167	0.1153	0.0723	0.0719	0.0741	0.0069	0.0201	0.098	-0.0023	-0.0225	0.0669	0.0706	0.0835	42.098	6.562	30.488
3	0.292	0.9461	-0.0176	4.4954	-2.6651	5.3546	-0.2358	0.0341	0.1782	-0.586	0.4461	0.6326	-0.1327	-0.5895	-0.2103	0.2695	0.0553	-0.1855	0.2433	0.0456	0.3056	23.65	34.89	-8.361
4	1.372	-0.1356	-0.3144	0.707	0.1246	0.8889	-0.0097	0.1605	-0.0107	-0.0703	0.0352	0.0532	0.0186	-0.0554	-0.0255	0.0588	-0.0011	-0.0673	0.0437	-0.0036	0.0788	37.403	21.521	-1.218
5	1.4605	0.1672	0.2246	0.9312	0.2645	2.6123	-0.064	-0.1356	-0.0752	0.0944	0.0047	0.1164	-0.266	-0.0978	0.0594	0.0748	0.0126	-0.0287	0.0342	0.0253	0.0871	28.9	23.366	21.296
6	2.1173	-0.5179	0.4921	1.9819	-0.078	1.2576	0.0873	0.1824	-0.2305	-0.0922	-0.1114	-0.3619	0.2752	0.4886	0.0241	0.1755	0.1442	-0.0287	0.2717	-0.0734	0.276	71.51	-3.501	2.815
7	0.7813	-0.1318	-0.3141	0.5776	-0.2731	1.8679	0.0542	0.0059	-0.259	0.0067	-0.0384	0.0133	0.2017	0.1734	-0.0157	0.0688	0.0382	-0.0585	0.0355	-0.0119	0.1266	60.504	0.197	12.802
8	0.9521	-0.2881	0.3798	2.3093	-0.7134	0.9361	0.0145	0.1989	-0.0659	-0.1672	0.0031	-0.0944	0.1277	0.0759	-0.0176	0.0673	0.0145	-0.0516	0.0665	-0.0422	0.0835	53.164	12.615	-3.013
9	1.6596	-0.5187	0.5658	0.7402	-0.2022	0.75	-0.0273	0.1	0.0131	-0.0309	0.0232	-0.041	-0.0388	0.137	0.0042	0.0218	-0.0168	-0.0288	0.0488	0.0118	0.0616	78.432	33.196	8.676
10	1.1637	0.4477	-0.5128	2.105	-0.8679	1.8735	-0.1069	-0.2347	-0.0723	0.0655	0.0137	-0.1436	0.1204	0.0809	0.0931	0.0711	0.0257	-0.0458	0.1097	0.012	0.0603	77.706	25.828	27.599
11	3.8257	-11.5559	-0.3871	35.1394	0.9387	0.2693	0.1334	0.0669	0.0964	-0.4707	-0.1729	-0.329	0.0424	-0.0349	0.0395	0.1036	0.057	-0.0189	0.1219	0.0498	0.1662	38.605	65.89	15.513
12	0.8942	0.1177	-0.1626	0.9786	-0.6209	1.8033	0.0335	-0.0805	0.2106	0.1113	-0.015	0.0014	-0.1004	-0.0065	-0.0186	0.0967	0.0225	-0.0495	0.0155	-0.0356	0.086	48.469	50.107	21.879
13	1.5608	-0.7187	-0.6671	1.7195	1.233	1.2172	0.0654	0.1938	0.0117	-0.0887	-0.1123	-0.0735	-0.0786	-0.0814	0.0468	0.0421	-0.0126	-0.045	0.0456	0.0351	0.0888	62.19	43.353	4.226
14	2.1021	-0.7558	-0.6105	0.8936	0.0024	1.1031	-0.1631	-0.4816	-0.0291	0.2929	0.1443	-0.1517	0.0676	0.111	0.0189	0.1998	0.0617	-0.0928	0.2434	0.012	0.0552	66.765	27.907	43.805
15	3.1556	-0.5876	0.3273	0.7532	-0.2673	0.7855	0.0125	-0.3389	0.043	0.1443	0.0372	0.0007	-0.0143	-0.0963	-0.0498	0.1722	0.018	-0.0589	0.0764	-0.0282	0.0398	49.173	40.165	37.591

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-5 - 8
2	X-RAY DIFFRACTION	2	A	9 - 161
3	X-RAY DIFFRACTION	2	A	162 - 243
4	X-RAY DIFFRACTION	3	B	-5 - 9
5	X-RAY DIFFRACTION	4	B	10 - 178
6	X-RAY DIFFRACTION	5	B	179 - 243
7	X-RAY DIFFRACTION	6	C	-4 - 44
8	X-RAY DIFFRACTION	7	C	45 - 162
9	X-RAY DIFFRACTION	8	C	163 - 243
10	X-RAY DIFFRACTION	9	D	0 - 161
11	X-RAY DIFFRACTION	10	D	162 - 242
12	X-RAY DIFFRACTION	11	E	-4 - 4
13	X-RAY DIFFRACTION	12	E	5 - 175
14	X-RAY DIFFRACTION	13	E	176 - 243
15	X-RAY DIFFRACTION	14	F	1 - 168
16	X-RAY DIFFRACTION	15	F	169 - 242

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