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- PDB-4fc6: Studies on DCR shed new light on peroxisomal beta-oxidation: Crys... -

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Basic information

Entry
Database: PDB / ID: 4fc6
TitleStudies on DCR shed new light on peroxisomal beta-oxidation: Crystal structure of the ternary complex of pDCR
ComponentsPeroxisomal 2,4-dienoyl-CoA reductase
KeywordsOXIDOREDUCTASE / SDR/Rossmann fold / peroxisomal beta-oxidation
Function / homology
Function and homology information


2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing] / 2,4-dienoyl-CoA reductase (NADPH) activity / trans-2-enoyl-CoA reductase (NADPH) activity / fatty acid beta-oxidation using acyl-CoA oxidase / unsaturated fatty acid biosynthetic process / Beta-oxidation of very long chain fatty acids / peroxisomal membrane / fatty acid metabolic process / Peroxisomal protein import / peroxisome / cytosol
Similarity search - Function
Peroxisomal 2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing] / PKS_KR / 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 / Peroxisomal 2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHua, T. / Wu, D. / Wang, J. / Shaw, N. / Liu, Z.-J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Studies of human 2,4-dienoyl CoA reductase shed new light on peroxisomal beta-oxidation of unsaturated fatty acids
Authors: Hua, T. / Wu, D. / Ding, W. / Wang, J. / Shaw, N. / Liu, Z.J.
History
DepositionMay 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Feb 28, 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

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Assembly

Deposited unit
A: Peroxisomal 2,4-dienoyl-CoA reductase
B: Peroxisomal 2,4-dienoyl-CoA reductase
C: Peroxisomal 2,4-dienoyl-CoA reductase
D: Peroxisomal 2,4-dienoyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,31112
Polymers116,8754
Non-polymers6,4368
Water14,034779
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25170 Å2
ΔGint-175 kcal/mol
Surface area31210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.038, 95.114, 133.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Peroxisomal 2,4-dienoyl-CoA reductase / pDCR / 2 / 4-dienoyl-CoA reductase 2


Mass: 29218.637 Da / Num. of mol.: 4 / Fragment: UNP residues 2-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DECR2, PDCR / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NUI1, 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.: 779 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6
Details: 0.1M MES (pH 6.0) and 8% PEG6000, VAPOR DIFFUSION, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9795 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 62674 / Num. obs: 60105 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→41.8 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.923 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21529 3196 5 %RANDOM
Rwork0.15586 ---
all0.159 62674 --
obs0.15883 60102 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.133 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8142 0 412 779 9333
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 190 -
Rwork0.179 3444 -
obs--75.65 %

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