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- PDB-9rgr: Crystal Structure of Rattus norvegicus Enoyl-CoA Hydratase in com... -

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Basic information

Entry
Database: PDB / ID: 9rgr
TitleCrystal Structure of Rattus norvegicus Enoyl-CoA Hydratase in complex with 3S-hydroxybutanoyl-CoA
Components(Enoyl-CoA hydratase, mitochondrial) x 2
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
3-HYDROXYBUTANOYL-COENZYME A / Enoyl-CoA hydratase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.69 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
C: Enoyl-CoA hydratase, mitochondrial
D: Enoyl-CoA hydratase, mitochondrial
E: Enoyl-CoA hydratase, mitochondrial
F: Enoyl-CoA hydratase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,63311
Polymers189,3646
Non-polymers4,2685
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38930 Å2
ΔGint-180 kcal/mol
Surface area51670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.114, 93.694, 247.474
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 31571.404 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: 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.: 4
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
#3: Chemical
ChemComp-3HC / 3-HYDROXYBUTANOYL-COENZYME A / 3-HYDROXYBUTYRYL-COENZYME A


Mass: 853.623 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C25H42N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 100mM Tris, pH 7.5, 2.43M (NH4)2SO4), 5%v/v octanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.5417 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Aug 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.69→72.75 Å / Num. obs: 49784 / % possible obs: 99.8 % / Redundancy: 8.6 % / Biso Wilson estimate: 21.88 Å2 / CC1/2: 0.979 / Rpim(I) all: 0.096 / Net I/σ(I): 7.6
Reflection shellResolution: 2.69→2.78 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4419 / CC1/2: 0.769 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→72.75 Å / SU ML: 0.349 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 24.2823
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2518 4433 4.71 %
Rwork0.2036 89692 -
obs0.2058 49710 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.26 Å2
Refinement stepCycle: LAST / Resolution: 2.69→72.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11639 0 270 71 11980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001612067
X-RAY DIFFRACTIONf_angle_d0.441716254
X-RAY DIFFRACTIONf_chiral_restr0.04081835
X-RAY DIFFRACTIONf_plane_restr0.00312094
X-RAY DIFFRACTIONf_dihedral_angle_d13.66734597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.730.36461180.29752862X-RAY DIFFRACTION94.81
2.73-2.760.3291480.27532978X-RAY DIFFRACTION99.71
2.76-2.790.35691490.27422973X-RAY DIFFRACTION99.81
2.79-2.830.33311370.27363055X-RAY DIFFRACTION99.78
2.83-2.860.30211370.27772939X-RAY DIFFRACTION99.81
2.86-2.90.28681400.25833049X-RAY DIFFRACTION99.94
2.9-2.940.33251710.26082997X-RAY DIFFRACTION100
2.94-2.990.29261500.25562966X-RAY DIFFRACTION99.97
2.99-3.030.32621350.24693061X-RAY DIFFRACTION100
3.03-3.080.29541560.23922980X-RAY DIFFRACTION100
3.08-3.140.2991550.22532935X-RAY DIFFRACTION100
3.14-3.190.26891560.22713022X-RAY DIFFRACTION100
3.19-3.260.27341300.22273013X-RAY DIFFRACTION100
3.26-3.320.26761290.21623059X-RAY DIFFRACTION100
3.32-3.390.28011370.21672966X-RAY DIFFRACTION99.97
3.39-3.470.24121560.20863039X-RAY DIFFRACTION99.97
3.47-3.560.26071410.20522971X-RAY DIFFRACTION100
3.56-3.660.2981750.20982967X-RAY DIFFRACTION100
3.66-3.760.2641460.20263031X-RAY DIFFRACTION100
3.76-3.890.28731720.19172976X-RAY DIFFRACTION100
3.89-4.020.20731800.17782965X-RAY DIFFRACTION100
4.03-4.190.2171400.17082981X-RAY DIFFRACTION100
4.19-4.380.16631610.1622982X-RAY DIFFRACTION100
4.38-4.610.21751690.1552978X-RAY DIFFRACTION100
4.61-4.90.17911310.15053009X-RAY DIFFRACTION99.97
4.9-5.270.18341350.15513033X-RAY DIFFRACTION99.91
5.27-5.80.27851390.19243003X-RAY DIFFRACTION99.81
5.8-6.640.23481440.1892996X-RAY DIFFRACTION99.62
6.64-8.360.17641440.15652997X-RAY DIFFRACTION99.87
8.37-72.750.1661520.14772909X-RAY DIFFRACTION97.24

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