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

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Basic information

Entry
Database: PDB / ID: 9rgt
TitleCrystal Structure of Rattus norvegicus Enoyl-CoA Hydratase in complex with 3S-hydroxydecanoyl-CoA
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
(S)-3-HYDROXYDECANOYL-COA / Enoyl-CoA hydratase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / 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
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)194,00111
Polymers189,3326
Non-polymers4,6695
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32640 Å2
ΔGint-195 kcal/mol
Surface area52730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.791, 94.480, 248.973
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: 31555.404 Da / Num. of mol.: 6
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-HSC / (S)-3-HYDROXYDECANOYL-COA


Mass: 933.751 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C31H50N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5 / Details: 100mM MES, pH 5.5, 2.1M (NH4)2SO4, 10% 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: Oct 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2→73.38 Å / Num. obs: 120103 / % possible obs: 97 % / Redundancy: 9.7 % / Biso Wilson estimate: 15.99 Å2 / CC1/2: 0.987 / Rpim(I) all: 0.04 / Net I/σ(I): 11
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4754 / CC1/2: 0.478 / % possible all: 78.7

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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→73.38 Å / SU ML: 0.2843 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 26.3504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2578 11044 5.06 %
Rwork0.2301 207011 -
obs0.2316 119681 91.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.84 Å2
Refinement stepCycle: LAST / Resolution: 2→73.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11672 0 300 574 12546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002612138
X-RAY DIFFRACTIONf_angle_d0.849916343
X-RAY DIFFRACTIONf_chiral_restr0.22811841
X-RAY DIFFRACTIONf_plane_restr0.00432099
X-RAY DIFFRACTIONf_dihedral_angle_d14.38474931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.32042280.3354193X-RAY DIFFRACTION55.35
2.02-2.040.32813190.32385808X-RAY DIFFRACTION78.35
2.04-2.070.38192870.32086181X-RAY DIFFRACTION80.74
2.07-2.090.33743190.32156134X-RAY DIFFRACTION81.7
2.09-2.120.30783570.31096269X-RAY DIFFRACTION83.71
2.12-2.150.30363280.29686434X-RAY DIFFRACTION84.77
2.15-2.180.3483250.30486388X-RAY DIFFRACTION84.61
2.18-2.210.31953130.30376372X-RAY DIFFRACTION84.43
2.21-2.250.44152660.4275303X-RAY DIFFRACTION69.92
2.25-2.280.45752650.39315473X-RAY DIFFRACTION72.75
2.28-2.320.29443810.25977069X-RAY DIFFRACTION94.01
2.32-2.370.26363400.24947223X-RAY DIFFRACTION95.01
2.37-2.410.28223950.24027183X-RAY DIFFRACTION95.9
2.41-2.460.26893780.23187324X-RAY DIFFRACTION96.81
2.46-2.510.27283660.22847353X-RAY DIFFRACTION97.44
2.51-2.570.26413920.22667428X-RAY DIFFRACTION98.61
2.57-2.640.27684060.23797485X-RAY DIFFRACTION99.08
2.64-2.710.27394100.23747442X-RAY DIFFRACTION99.17
2.71-2.790.28334030.22947468X-RAY DIFFRACTION99.62
2.79-2.880.26744170.2317523X-RAY DIFFRACTION99.94
2.88-2.980.27224650.22877479X-RAY DIFFRACTION100
2.98-3.10.26693440.21357568X-RAY DIFFRACTION100
3.1-3.240.2454570.2167480X-RAY DIFFRACTION100
3.24-3.410.25514160.21887524X-RAY DIFFRACTION100
3.41-3.630.23663950.19947536X-RAY DIFFRACTION99.8
3.63-3.910.24784510.22537367X-RAY DIFFRACTION98.7
3.91-4.30.17764190.16497544X-RAY DIFFRACTION99.99
4.3-4.920.16184000.14957488X-RAY DIFFRACTION99.95
4.92-6.20.19553610.17727583X-RAY DIFFRACTION99.97
6.2-73.380.18154410.16587389X-RAY DIFFRACTION98.64

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