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- PDB-1w6u: Structure of human DECR ternary complex -

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Basic information

Entry
Database: PDB / ID: 1w6u
TitleStructure of human DECR ternary complex
Components2,4-DIENOYL-COA REDUCTASE, MITOCHONDRIAL PRECURSOR
KeywordsOXIDOREDUCTASE / DIENOYL COA-REDUCTASE / SHORT CHAIN DEHYDROGENASE / BETA-OXIDATION / NADP / REDUCTASE
Function / homology
Function and homology information


2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing] / 2,4-dienoyl-CoA reductase (NADPH) activity / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / fatty acid beta-oxidation / catalytic complex / NADPH binding / positive regulation of cold-induced thermogenesis / mitochondrial matrix / mitochondrion / nucleoplasm ...2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing] / 2,4-dienoyl-CoA reductase (NADPH) activity / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / fatty acid beta-oxidation / catalytic complex / NADPH binding / positive regulation of cold-induced thermogenesis / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HEXANOYL-COENZYME A / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing], mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.75 Å
AuthorsAlphey, M.S. / Byres, E. / Li, D. / Hunter, W.N.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure and Reactivity of Human Mitochondrial 2,4-Dienoyl-Coa Reductase: Enzyme-Ligand Interactions in a Distinctive Short-Chain Reductase Active Site
Authors: Alphey, M.S. / Yu, W. / Byres, E. / Li, D. / Hunter, W.N.
History
DepositionAug 24, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,4-DIENOYL-COA REDUCTASE, MITOCHONDRIAL PRECURSOR
B: 2,4-DIENOYL-COA REDUCTASE, MITOCHONDRIAL PRECURSOR
C: 2,4-DIENOYL-COA REDUCTASE, MITOCHONDRIAL PRECURSOR
D: 2,4-DIENOYL-COA REDUCTASE, MITOCHONDRIAL PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,69712
Polymers129,2604
Non-polymers6,4368
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.281, 131.658, 70.849
Angle α, β, γ (deg.)90.00, 92.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.852879, 0.522053, 0.007676), (0.522105, 0.852721, 0.016501), (0.002069, 0.01808, -0.999834)32.3218, -9.1879, 4.8496
2given(-0.999986, 0.000474, -0.005363), (-0.000357, -0.999763, -0.021772), (-0.005372, -0.021769, 0.999749)31.5967, -11.8723, -0.0592
3given(0.85486, -0.518854, -0.002393), (-0.518849, -0.854863, 0.002183), (-0.003178, -0.000624, -0.999995)-0.8152, -2.8945, 4.9085

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Components

#1: Protein
2,4-DIENOYL-COA REDUCTASE, MITOCHONDRIAL PRECURSOR / 2 / 4-DIENOYL-COA REDUCTASE [NADPH] / 4-ENOYL-COA REDUCTASE [NADPH]


Mass: 32315.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: COFACTOR (N) NADP SUBSTRATE (S) 2,4-HEXADIENOYL-COA
Source: (gene. exp.) HOMO SAPIENS (human) / Organelle: MITOCHONDRIAL / Plasmid: PLM1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q16698, 2,4-dienoyl-CoA reductase [(2E)-enoyl-CoA-producing]
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-HXC / HEXANOYL-COENZYME A


Mass: 865.677 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46N7O17P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: TRANS-2,3-DIDEHYDROACYL-COA + NADP(+)= TRANS,TRANS-2,3,4,5-TETRADEHYDROACYL-COA + NADPH.

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.4 / Details: pH 7.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9756
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 7, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) OR SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 110749 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.1
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.2 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.75→70.71 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.03 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.268 5590 5 %RANDOM
Rwork0.227 ---
obs0.229 105117 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.29 Å2
Baniso -1Baniso -2Baniso -3
1-3.78 Å20 Å21.14 Å2
2---0.63 Å20 Å2
3----3.04 Å2
Refinement stepCycle: LAST / Resolution: 1.75→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8527 0 412 580 9519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229242
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1552.01312586
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2951133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.21460
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026623
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1840.24941
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4671.55649
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.85129086
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.99233593
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.644.53484
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.8 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.365 400
Rwork0.357 7197

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