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- PDB-9rgq: Crystal Structure of Rattus norvegicus Enoyl-CoA Hydratase in unl... -

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Basic information

Entry
Database: PDB / ID: 9rgq
TitleCrystal Structure of Rattus norvegicus Enoyl-CoA Hydratase in unliganded form
ComponentsEnoyl-CoA hydratase, mitochondrial
KeywordsLYASE / crotonase / hydratase / beta-oxidation
Function / homology
Function and homology information


Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / 3-hydroxypropionyl-CoA dehydratase activity / (2E)-butenoyl-CoA hydratase activity / Branched-chain amino acid catabolism / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity ...Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / 3-hydroxypropionyl-CoA dehydratase activity / (2E)-butenoyl-CoA hydratase activity / Branched-chain amino acid catabolism / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / enoyl-CoA hydratase / enoyl-CoA hydratase activity / fatty acid beta-oxidation / mitochondrial matrix / mitochondrion
Similarity search - Function
Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Enoyl-CoA hydratase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDalwani, S. / Wierenga, R.K.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland Finland
Finnish Cultural Foundation Finland
CitationJournal: Jacs Au / Year: 2026
Title: Enantioselective Hydration of Non-CoA Enoyl-Thioesters by Enoyl-CoA Hydratase (ECH): Activation of the Active Site Oxyanion Hole with 3',5'-Adenosine-Diphosphate Enables Competent Catalysis.
Authors: Dalwani, S. / Mondal, P.K. / Schmitz, W. / Wierenga, R.K. / Pihko, P.M.
History
DepositionJun 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-CoA hydratase, mitochondrial
B: Enoyl-CoA hydratase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6818
Polymers63,1112
Non-polymers5706
Water2,000111
1
A: Enoyl-CoA hydratase, mitochondrial
B: Enoyl-CoA hydratase, mitochondrial
hetero molecules

A: Enoyl-CoA hydratase, mitochondrial
B: Enoyl-CoA hydratase, mitochondrial
hetero molecules

A: Enoyl-CoA hydratase, mitochondrial
B: Enoyl-CoA hydratase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,04224
Polymers189,3326
Non-polymers1,70918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area35260 Å2
ΔGint-285 kcal/mol
Surface area52050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.397, 77.397, 217.287
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-303-

PO4

21A-303-

PO4

31B-303-

PO4

41B-303-

PO4

51A-449-

HOH

61A-456-

HOH

71B-405-

HOH

81B-449-

HOH

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Components

#1: Protein Enoyl-CoA hydratase, mitochondrial / mECH / mECH1 / Enoyl-CoA hydratase 1 / ECHS1 / Short-chain enoyl-CoA hydratase / SCEH


Mass: 31555.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Echs1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P14604, enoyl-CoA hydratase, Delta3-Delta2-enoyl-CoA isomerase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 0.05M Calcium acetate hydrate; 0.1M Sodium cacodylate, pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.619913 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.619913 Å / Relative weight: 1
ReflectionResolution: 2→37.9 Å / Num. obs: 32842 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 48.14 Å2 / CC1/2: 0.99 / Net I/σ(I): 16.3
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 26562 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→36.46 Å / SU ML: 0.2797 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.7545
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2441 1587 4.83 %
Rwork0.1977 31237 -
obs0.1998 32824 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.97 Å2
Refinement stepCycle: LAST / Resolution: 2→36.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 30 111 4091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224028
X-RAY DIFFRACTIONf_angle_d0.43785418
X-RAY DIFFRACTIONf_chiral_restr0.0419608
X-RAY DIFFRACTIONf_plane_restr0.0038702
X-RAY DIFFRACTIONf_dihedral_angle_d4.6518548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.38561700.30682821X-RAY DIFFRACTION99.87
2.06-2.140.32131660.28222824X-RAY DIFFRACTION100
2.14-2.220.35071290.26172860X-RAY DIFFRACTION100
2.22-2.330.30381420.25972838X-RAY DIFFRACTION99.97
2.33-2.450.29341380.25612851X-RAY DIFFRACTION100
2.45-2.60.30141480.25592825X-RAY DIFFRACTION99.93
2.6-2.80.27121410.25832829X-RAY DIFFRACTION99.93
2.8-3.080.27481470.25042842X-RAY DIFFRACTION99.97
3.08-3.530.25911140.21472876X-RAY DIFFRACTION100
3.53-4.450.20741570.16872824X-RAY DIFFRACTION100
4.45-36.460.20361350.14852847X-RAY DIFFRACTION99.8

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