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- PDB-2hw5: The crystal structure of human enoyl-coenzyme A (CoA) hydratase s... -

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Basic information

Entry
Database: PDB / ID: 2hw5
TitleThe crystal structure of human enoyl-coenzyme A (CoA) hydratase short chain 1, ECHS1
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / fatty acid metabolism / hydratase/isomerase superfamily / Beta-oxidation / CoA / enoyl-CoA hydratase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / enoyl-CoA hydratase / Branched-chain amino acid catabolism / enoyl-CoA hydratase activity / fatty acid beta-oxidation / mitochondrial matrix / mitochondrion
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, conserved site / Enoyl-CoA hydratase/isomerase signature. / 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 ...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, conserved site / Enoyl-CoA hydratase/isomerase signature. / 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
CROTONYL COENZYME A / Enoyl-CoA hydratase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsTurnbull, A.P. / Salah, E. / Niesen, F. / Debreczeni, J. / Ugochukwu, E. / Pike, A.C.W. / Kavanagh, K. / Gileadi, O. / Gorrec, F. / Umeano, C. ...Turnbull, A.P. / Salah, E. / Niesen, F. / Debreczeni, J. / Ugochukwu, E. / Pike, A.C.W. / Kavanagh, K. / Gileadi, O. / Gorrec, F. / Umeano, C. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human enoyl-coenzyme A (CoA) hydratase short chain 1, ECHS1
Authors: Turnbull, A.P. / Salah, E. / Niesen, F. / Debreczeni, J. / Ugochukwu, E. / Pike, A.C.W. / Kavanagh, K. / Gileadi, O. / Gorrec, F. / Umeano, C. / von Delft, F. / Weigelt, J. / Edwards, A. / ...Authors: Turnbull, A.P. / Salah, E. / Niesen, F. / Debreczeni, J. / Ugochukwu, E. / Pike, A.C.W. / Kavanagh, K. / Gileadi, O. / Gorrec, F. / Umeano, C. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Oppermann, U.
History
DepositionJul 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)188,23412
Polymers186,4666
Non-polymers1,7686
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31590 Å2
ΔGint-245 kcal/mol
Surface area51700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.554, 97.344, 231.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Enoyl-CoA hydratase / / Short chain enoyl-CoA hydratase / SCEH / Enoyl-CoA hydratase 1


Mass: 31077.586 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ECHS1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)R3 / References: UniProt: P30084, enoyl-CoA hydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-COO / CROTONYL COENZYME A


Mass: 835.608 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O17P3S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M sodium formate, 0.1M Bis-Tris propane, 20 % PEG3350, 10 % Ethylene Glycol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. all: 66696 / Num. obs: 66696 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.55→2.64 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DUB

1dub


Resolution: 2.55→29.6 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 24.35 / SU ML: 0.237 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.462 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25165 3359 5 %RANDOM
Rwork0.21425 ---
all0.21614 63265 --
obs0.21614 63265 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.522 Å2
Baniso -1Baniso -2Baniso -3
1-4.79 Å20 Å20 Å2
2---2.73 Å20 Å2
3----2.06 Å2
Refinement stepCycle: LAST / Resolution: 2.55→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11455 0 74 0 11529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211715
X-RAY DIFFRACTIONr_bond_other_d0.0010.027600
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.96915858
X-RAY DIFFRACTIONr_angle_other_deg0.846318676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82151562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97325.665466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.344151952
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0441541
X-RAY DIFFRACTIONr_chiral_restr0.0620.21854
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213281
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022220
X-RAY DIFFRACTIONr_nbd_refined0.2070.22549
X-RAY DIFFRACTIONr_nbd_other0.1760.27840
X-RAY DIFFRACTIONr_nbtor_refined0.1740.26012
X-RAY DIFFRACTIONr_nbtor_other0.0860.25971
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2247
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0790.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4051.57976
X-RAY DIFFRACTIONr_mcbond_other0.0641.53208
X-RAY DIFFRACTIONr_mcangle_it0.684212248
X-RAY DIFFRACTIONr_scbond_it1.06134250
X-RAY DIFFRACTIONr_scangle_it1.7154.53606
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 246 -
Rwork0.313 4527 -
obs--96.06 %
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)
11.2171-0.3858-0.3941.2845-0.51491.59630.08130.08410.13480.0697-0.05630.2471-0.0983-0.4204-0.0251-0.221-0.00590.0586-0.1745-0.0892-0.0931-20.180574.458568.7048
21.2646-0.2467-0.66381.1858-0.43741.90430.0487-0.3639-0.11580.2883-0.1058-0.15210.2120.15310.0571-0.0985-0.12820.0086-0.20660.0015-0.1419-6.068133.432980.0081
31.7755-0.4717-0.51160.88260.3381.47350.16420.16210.1119-0.0722-0.14890.23920.064-0.4921-0.0153-0.2083-0.07760.0446-0.0723-0.047-0.0847-31.350543.324663.4931
41.26360.091-0.44780.5614-0.93592.23020.0835-0.26430.09120.3402-0.2097-0.26110.02130.2560.1262-0.0735-0.0865-0.0176-0.1531-0.0642-0.09731.179664.48390.0113
52.20070.15360.58591.2115-0.25152.24670.017-0.5299-0.11870.4739-0.01260.33020.1658-0.6804-0.00440.0658-0.2150.20860.1297-0.0235-0.0509-33.908537.300394.8131
61.86570.16210.30131.25970.38041.8788-0.0031-0.44240.09770.5539-0.10310.3002-0.1407-0.41280.10630.0773-0.05140.20560.053-0.1751-0.0907-29.013570.331899.303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA31 - 29027 - 286
2X-RAY DIFFRACTION2BB31 - 29027 - 286
3X-RAY DIFFRACTION3CC31 - 29027 - 286
4X-RAY DIFFRACTION4DD31 - 29027 - 286
5X-RAY DIFFRACTION5EE31 - 29027 - 286
6X-RAY DIFFRACTION6FF31 - 29027 - 286

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