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

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Basic information

Entry
Database: PDB / ID: 4jyl
TitleCrystal structure of enoyl-CoA hydratase from Thermoplasma volcanium GSS1
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / hydratase
Function / homology
Function and homology information


fatty acid beta-oxidation
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.37 Å
AuthorsShabalin, I.G. / Cooper, D.R. / Majorek, K.A. / Mikolajczak, K. / Porebski, P.J. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Bonanno, J. / Seidel, R. ...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 Structural Genomics Research Consortium (NYSGRC)
CitationJournal: 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 ...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 Structural Genomics Research Consortium (NYSGRC)
History
DepositionMar 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: 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
Revision 1.2Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)177,14713
Polymers176,8396
Non-polymers3097
Water12,016667
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31530 Å2
ΔGint-260 kcal/mol
Surface area46940 Å2
MethodPISA
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 number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLYSLYSAA-5 - 24317 - 265
21ASNASNLYSLYSBB-5 - 24317 - 265
12LEULEUARGARGAA-4 - 24218 - 264
22LEULEUARGARGCC-4 - 24218 - 264
13SERSERTRPTRPAA0 - 24122 - 263
23SERSERTRPTRPDD0 - 24122 - 263
14LEULEUARGARGAA-4 - 24218 - 264
24LEULEUARGARGEE-4 - 24218 - 264
15MSEMSETRPTRPAA1 - 24123 - 263
25MSEMSETRPTRPFF1 - 24123 - 263
16LEULEUARGARGBB-4 - 24218 - 264
26LEULEUARGARGCC-4 - 24218 - 264
17SERSERTRPTRPBB0 - 24122 - 263
27SERSERTRPTRPDD0 - 24122 - 263
18LEULEUARGARGBB-4 - 24218 - 264
28LEULEUARGARGEE-4 - 24218 - 264
19MSEMSETRPTRPBB1 - 24123 - 263
29MSEMSETRPTRPFF1 - 24123 - 263
110SERSERTRPTRPCC0 - 24122 - 263
210SERSERTRPTRPDD0 - 24122 - 263
111LEULEULYSLYSCC-4 - 24318 - 265
211LEULEULYSLYSEE-4 - 24318 - 265
112MSEMSETRPTRPCC1 - 24123 - 263
212MSEMSETRPTRPFF1 - 24123 - 263
113SERSERTRPTRPDD0 - 24122 - 263
213SERSERTRPTRPEE0 - 24122 - 263
114MSEMSETRPTRPDD1 - 24123 - 263
214MSEMSETRPTRPFF1 - 24123 - 263
115MSEMSETRPTRPEE1 - 24123 - 263
215MSEMSETRPTRPFF1 - 24123 - 263

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

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Components

#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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2013 / Details: C(111)
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 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 % / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.165 / Rsym value: 0.165 / Χ2: 3.595 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
2.37-2.413.70.681.933870.680.72599.1
2.41-2.453.70.56933900.74399.4
2.45-2.53.70.50334230.7399.6
2.5-2.553.80.4533720.77999.6
2.55-2.613.90.40334160.81199.5
2.61-2.6740.3534200.80599.7
2.67-2.744.20.31233950.91299.9
2.74-2.814.50.27634010.997100
2.81-2.894.90.24134271.138100
2.89-2.995.40.21934231.28100
2.99-3.095.70.18934511.513100
3.09-3.225.80.16933841.761100
3.22-3.365.80.14934292.165100
3.36-3.545.40.14534632.824100
3.54-3.762.80.388340437.62499.9
3.76-4.054.40.12334475.04499.9
4.05-4.465.80.11334316.209100
4.46-5.15.70.09934485.54499.9
5.1-6.435.80.09434634.273100
6.43-505.60.08135158.0299.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
SHELXphasing
MLPHAREphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.37→45.78 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1698 / WRfactor Rwork: 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 Rfree: 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
RfactorNum. reflection% reflectionSelection details
Rfree0.1905 3464 5.1 %RANDOM
Rwork0.1573 ---
all0.1589 68596 --
obs0.1589 68445 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 108.51 Å2 / Biso mean: 31.6749 Å2 / Biso min: 7.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å2-0 Å21.64 Å2
2---0.47 Å2-0 Å2
3---1.67 Å2
Refinement stepCycle: LAST / Resolution: 2.37→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11247 0 11 667 11925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01911477
X-RAY DIFFRACTIONr_bond_other_d0.0090.0211426
X-RAY DIFFRACTIONr_angle_refined_deg1.7172.00715449
X-RAY DIFFRACTIONr_angle_other_deg1.372326345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95351492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02224.774465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.542151997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9821573
X-RAY DIFFRACTIONr_chiral_restr0.0920.21759
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212930
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022383
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A148460.09
12B148460.09
21A148100.08
22C148100.08
31A145770.07
32D145770.07
41A148040.08
42E148040.08
51A147290.06
52F147290.06
61B146420.09
62C146420.09
71B143870.08
72D143870.08
81B146520.09
82E146520.09
91B144940.08
92F144940.08
101C145920.08
102D145920.08
111C147700.09
112E147700.09
121C146390.07
122F146390.07
131D146800.07
132E146800.07
141D145740.07
142F145740.07
151E145420.08
152F145420.08
LS refinement shellResolution: 2.37→2.431 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 255 -
Rwork0.24 4751 -
all-5006 -
obs-4751 99.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
15.11892.8804-8.86661.6398-4.999115.3982-0.1473-0.9142-0.2794-0.0828-0.4159-0.11680.35821.55830.56310.52590.12250.11680.6850.31380.532435.062-0.09648.678
21.5683-0.5745-0.160.91380.0710.8214-0.0923-0.2538-0.21670.11530.07230.07190.07410.00690.02010.098-0.0023-0.02250.06690.07060.083542.0986.56230.488
30.2920.9461-0.01764.4954-2.66515.3546-0.23580.03410.1782-0.5860.44610.6326-0.1327-0.5895-0.21030.26950.0553-0.18550.24330.04560.305623.6534.89-8.361
41.372-0.1356-0.31440.7070.12460.8889-0.00970.1605-0.0107-0.07030.03520.05320.0186-0.0554-0.02550.0588-0.0011-0.06730.0437-0.00360.078837.40321.521-1.218
51.46050.16720.22460.93120.26452.6123-0.064-0.1356-0.07520.09440.00470.1164-0.266-0.09780.05940.07480.0126-0.02870.03420.02530.087128.923.36621.296
62.1173-0.51790.49211.9819-0.0781.25760.08730.1824-0.2305-0.0922-0.1114-0.36190.27520.48860.02410.17550.1442-0.02870.2717-0.07340.27671.51-3.5012.815
70.7813-0.1318-0.31410.5776-0.27311.86790.05420.0059-0.2590.0067-0.03840.01330.20170.1734-0.01570.06880.0382-0.05850.0355-0.01190.126660.5040.19712.802
80.9521-0.28810.37982.3093-0.71340.93610.01450.1989-0.0659-0.16720.0031-0.09440.12770.0759-0.01760.06730.0145-0.05160.0665-0.04220.083553.16412.615-3.013
91.6596-0.51870.56580.7402-0.20220.75-0.02730.10.0131-0.03090.0232-0.041-0.03880.1370.00420.0218-0.0168-0.02880.04880.01180.061678.43233.1968.676
101.16370.4477-0.51282.105-0.86791.8735-0.1069-0.2347-0.07230.06550.0137-0.14360.12040.08090.09310.07110.0257-0.04580.10970.0120.060377.70625.82827.599
113.8257-11.5559-0.387135.13940.93870.26930.13340.06690.0964-0.4707-0.1729-0.3290.0424-0.03490.03950.10360.057-0.01890.12190.04980.166238.60565.8915.513
120.89420.1177-0.16260.9786-0.62091.80330.0335-0.08050.21060.1113-0.0150.0014-0.1004-0.0065-0.01860.09670.0225-0.04950.0155-0.03560.08648.46950.10721.879
131.5608-0.7187-0.66711.71951.2331.21720.06540.19380.0117-0.0887-0.1123-0.0735-0.0786-0.08140.04680.0421-0.0126-0.0450.04560.03510.088862.1943.3534.226
142.1021-0.7558-0.61050.89360.00241.1031-0.1631-0.4816-0.02910.29290.1443-0.15170.06760.1110.01890.19980.0617-0.09280.24340.0120.055266.76527.90743.805
153.1556-0.58760.32730.7532-0.26730.78550.0125-0.33890.0430.14430.03720.0007-0.0143-0.0963-0.04980.17220.018-0.05890.0764-0.02820.039849.17340.16537.591
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 8
2X-RAY DIFFRACTION2A9 - 161
3X-RAY DIFFRACTION2A162 - 243
4X-RAY DIFFRACTION3B-5 - 9
5X-RAY DIFFRACTION4B10 - 178
6X-RAY DIFFRACTION5B179 - 243
7X-RAY DIFFRACTION6C-4 - 44
8X-RAY DIFFRACTION7C45 - 162
9X-RAY DIFFRACTION8C163 - 243
10X-RAY DIFFRACTION9D0 - 161
11X-RAY DIFFRACTION10D162 - 242
12X-RAY DIFFRACTION11E-4 - 4
13X-RAY DIFFRACTION12E5 - 175
14X-RAY DIFFRACTION13E176 - 243
15X-RAY DIFFRACTION14F1 - 168
16X-RAY DIFFRACTION15F169 - 242

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