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

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Basic information

Entry
Database: PDB / ID: 9rgu
TitleCrystal Structure of Rattus norvegicus Enoyl-CoA Hydratase in complex with 3S hydroxyhexanoyl-PAN and 3',5', diphosphate adenosine
Components(Enoyl-CoA hydratase, ...) x 4
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
: / ADENOSINE-3'-5'-DIPHOSPHATE / COENZYME A / Enoyl-CoA hydratase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

Downloads & links

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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)194,29016
Polymers189,4766
Non-polymers4,81410
Water8,827490
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.833, 92.997, 247.469
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Enoyl-CoA hydratase, ... , 4 types, 6 molecules AFBCDE

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


Mass: 31587.404 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: 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
#3: Protein Enoyl-CoA hydratase, mitochondrial / mECH / mECH1 / Enoyl-CoA hydratase 1 / ECHS1 / Short-chain enoyl-CoA hydratase / SCEH


Mass: 31587.404 Da / Num. of mol.: 1
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
#4: 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.: 1
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

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Non-polymers , 4 types, 500 molecules

#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Chemical
ChemComp-A1JF6 / ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2,4-bis(oxidanyl)butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanylhexanethioate


Mass: 392.511 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H32N2O6S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 100mM Tris, pH 7.5, 2.1M (NH4)2SO4, 10% octanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.729 Å
DetectorType: DECTRIS EIGER2 XE CdTe 16M / Detector: PIXEL / Date: Oct 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.729 Å / Relative weight: 1
ReflectionResolution: 1.7→47.9 Å / Num. obs: 192681 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rpim(I) all: 0.037 / Net I/σ(I): 14
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9478 / CC1/2: 0.34

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.723 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.112
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2476 9602 4.987 %
Rwork0.217 182920 -
all0.219 --
obs-192522 99.927 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.196 Å20 Å20 Å2
2--2.677 Å2-0 Å2
3----2.48 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11571 0 308 490 12369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01212108
X-RAY DIFFRACTIONr_angle_refined_deg0.9491.65316318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75251538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17923.993561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.491152177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3491554
X-RAY DIFFRACTIONr_chiral_restr0.0730.21642
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028920
X-RAY DIFFRACTIONr_nbd_refined0.1860.25749
X-RAY DIFFRACTIONr_nbtor_refined0.3030.28228
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2766
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1590.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1060.214
X-RAY DIFFRACTIONr_mcbond_it1.3223.3026128
X-RAY DIFFRACTIONr_mcangle_it2.1524.9357650
X-RAY DIFFRACTIONr_scbond_it1.8933.7815980
X-RAY DIFFRACTIONr_scangle_it3.145.5588660
X-RAY DIFFRACTIONr_lrange_it5.46646.18218342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.397330.38813372X-RAY DIFFRACTION99.9008
1.744-1.7920.3516530.36313130X-RAY DIFFRACTION99.9855
1.792-1.8440.3366800.33312671X-RAY DIFFRACTION100
1.844-1.9010.3086640.30612363X-RAY DIFFRACTION99.9923
1.901-1.9630.2866210.27311935X-RAY DIFFRACTION99.992
1.963-2.0320.2696370.25211591X-RAY DIFFRACTION99.9836
2.032-2.1090.2575550.23211265X-RAY DIFFRACTION99.9831
2.109-2.1950.2435800.21810736X-RAY DIFFRACTION99.9912
2.195-2.2920.2455360.21610358X-RAY DIFFRACTION99.7893
2.292-2.4040.2595340.2259891X-RAY DIFFRACTION100
2.404-2.5340.2685220.2069438X-RAY DIFFRACTION99.9799
2.534-2.6880.2684770.2198916X-RAY DIFFRACTION99.9787
2.688-2.8730.2594260.2268464X-RAY DIFFRACTION100
2.873-3.1040.2654270.2257846X-RAY DIFFRACTION100
3.104-3.40.2363750.1967253X-RAY DIFFRACTION99.9738
3.4-3.8010.2133280.1786640X-RAY DIFFRACTION100
3.801-4.3890.2012780.1665864X-RAY DIFFRACTION100
4.389-5.3750.1782500.1685008X-RAY DIFFRACTION100
5.375-7.5990.2452140.213926X-RAY DIFFRACTION100

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