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- PDB-1mj3: Crystal Structure Analysis of rat enoyl-CoA hydratase in complex ... -

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Basic information

Entry
Database: PDB / ID: 1mj3
TitleCrystal Structure Analysis of rat enoyl-CoA hydratase in complex with hexadienoyl-CoA
ComponentsENOYL-COA HYDRATASE, MITOCHONDRIAL
KeywordsLYASE / Homohexamer
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 / 3-hydroxypropionyl-CoA dehydratase activity / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / crotonyl-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 / 3-hydroxypropionyl-CoA dehydratase activity / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / crotonyl-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
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
HEXANOYL-COENZYME A / Enoyl-CoA hydratase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsBell, A.F. / Feng, Y. / Hofstein, H.A. / Parikh, S. / Wu, J. / Rudolph, M.J. / Kisker, C. / Tonge, P.J.
CitationJournal: Chem.Biol. / Year: 2002
Title: Stereoselectivity of Enoyl-CoA Hydratase Results from Preferential Activation of One of Two Bound Substrate Conformers
Authors: Bell, A.F. / Feng, Y. / Hofstein, H.A. / Parikh, S. / Wu, J. / Rudolph, M.J. / Kisker, C. / Whitty, A. / Tonge, P.J.
History
DepositionAug 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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, 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)173,91511
Polymers169,5876
Non-polymers4,3285
Water16,556919
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39140 Å2
ΔGint-236 kcal/mol
Surface area53170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.877, 95.198, 249.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homohexamer which is found in the asymetric unit

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Components

#1: Protein
ENOYL-COA HYDRATASE, MITOCHONDRIAL / / Short chain enoyl-CoA hydratase / Enoyl-CoA hydratase 1 / SCEH


Mass: 28264.461 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P14604, enoyl-CoA hydratase
#2: Chemical
ChemComp-HXC / HEXANOYL-COENZYME A


Mass: 865.677 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C27H46N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 919 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: ammonium sulfate, DTT, EDTA, n-octanol, MES, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.100 mMprotein1drop
21 mMHD-CoA1drop
32.4 Mammonium sulfate1reservoir
41 mMdithiothreitol1reservoir
51 mMEDTA1reservoir
65 %n-octanol1reservoir
7100 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2002
RadiationMonochromator: Platinum / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 96809 / % possible obs: 90.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.18 Å / % possible all: 78.5
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 97058 / % possible obs: 90.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 78.5 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
FFTmodel building
REFMAC5.1.24refinement
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→48.8 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.801 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.215 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22964 4801 4.9 %RANDOM
Rwork0.17238 ---
all0.1752 97057 --
obs0.1752 92256 90.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.079 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11730 0 275 919 12924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.02212160
X-RAY DIFFRACTIONr_angle_refined_deg2.5931.98916355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18251536
X-RAY DIFFRACTIONr_chiral_restr0.1820.21857
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028882
X-RAY DIFFRACTIONr_nbd_refined0.2460.25768
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2908
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4930.2127
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4910.233
X-RAY DIFFRACTIONr_mcbond_it2.9251.57632
X-RAY DIFFRACTIONr_mcangle_it4.588212126
X-RAY DIFFRACTIONr_scbond_it7.87234528
X-RAY DIFFRACTIONr_scangle_it12.3944.54229
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.306 322
Rwork0.222 5820
Refinement
*PLUS
Num. reflection obs: 92257 / % reflection Rfree: 5 % / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg3
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg5.3
X-RAY DIFFRACTIONr_planar_d0.013
X-RAY DIFFRACTIONr_chiral_restr0.18

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