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- PDB-1w73: Binary structure of human DECR solved by SeMet SAD. -

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Basic information

Entry
Database: PDB / ID: 1w73
TitleBinary structure of human DECR solved by SeMet SAD.
Components2,4-DIENOYL-COA REDUCTASE
KeywordsOXIDOREDUCTASE / SHORT CHAIN DEHYDROGENASE / REDUCTASE / SELENOMETHIONINE / SAD / DIENOYL-COA
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
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 / SAD / Resolution: 2.1 Å
AuthorsAlphey, M.S. / Byres, E. / 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 27, 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 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)133,91910
Polymers130,7614
Non-polymers3,1586
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.948, 131.737, 71.295
Angle α, β, γ (deg.)90.00, 92.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.867767, 0.496932, 0.006203), (0.496961, 0.867604, 0.017109), (0.003121, 0.017929, -0.999834)32.3861, -8.6319, 5.0431
2given(-0.999995, 0.000383, -0.002993), (-0.000317, -0.999761, -0.021848), (-0.003001, -0.021847, 0.999757)31.4596, -11.8316, -0.0933
3given(0.868061, -0.496447, -0.003356), (-0.496453, -0.868062, -0.001355), (-0.002241, 0.002843, -0.999993)-0.86, -3.2922, 5.0787

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Components

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


Mass: 32690.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organelle: MITOCHONDRIA / Plasmid: PLM1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q16698, 2,4-dienoyl-CoA reductase [(2E)-enoyl-CoA-producing]
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.4 / Details: pH 7.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 7, 2003 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→70 Å / Num. obs: 67331 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→70.71 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.795 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED LOOP (RESIDUES 240 TO 255) HAS BEEN OMITTED IN THE FOUR SUBUNITS. DISORDERED RESIDUES AT THE N- AND C-TERMINI HAVE BEEN OMITTED FROM THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3302 5.16 %RANDOM
Rwork0.18 ---
obs0.183 61874 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 29.34 Å2
Baniso -1Baniso -2Baniso -3
1-3.101 Å20 Å20.88 Å2
2---0.952 Å20 Å2
3----2.072 Å2
Refinement stepCycle: LAST / Resolution: 2.1→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8488 0 204 527 9219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228925
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.98112104
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73251125
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_restr0.0930.21403
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026472
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.24461
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.26097
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2581
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.320.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6351.55607
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2429022
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.24733318
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.594.53082
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.276 200
Rwork0.247 4303

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