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- PDB-1guf: Enoyl thioester reductase from Candida tropicalis -

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Basic information

Entry
Database: PDB / ID: 1guf
TitleEnoyl thioester reductase from Candida tropicalis
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH, B-SPECIFIC] 1, MITOCHONDRIAL
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADPH) / trans-2-enoyl-CoA reductase (NADPH) activity / fatty acid metabolic process / fatty acid biosynthetic process / mitochondrion
Similarity search - Function
Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex ...Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial
Similarity search - Component
Biological speciesCANDIDA TROPICALIS (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsAirenne, T.T. / Torkko, J.M. / Van Der Plas, S. / Sormunen, R.T. / Kastaniotis, A.J. / Wierenga, R.K. / Hiltunen, J.K.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structure-Function Analysis of Enoyl Thioester Reductase Involved in Mitochondrial Maintenance
Authors: Airenne, T.T. / Torkko, J.M. / Van Der Plas, S. / Sormunen, R.T. / Kastaniotis, A.J. / Wierenga, R.K. / Hiltunen, J.K.
History
DepositionJan 25, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2003Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH, B-SPECIFIC] 1, MITOCHONDRIAL
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH, B-SPECIFIC] 1, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,83117
Polymers79,1112
Non-polymers2,72015
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-105.1 kcal/mol
Surface area30140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.170, 92.170, 225.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.721, 0.6687, -0.1816), (0.6801, 0.6329, -0.37), (-0.1325, -0.3903, -0.9111)
Vector: 134.7482, -38.9412, 71.6938)

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Components

#1: Protein ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH, B-SPECIFIC] 1, MITOCHONDRIAL / 2 / 4-DIENOYL-COA REDUCTASE / TRANS-2-ENOYL-COA REDUCTASE 1 / 2-ENOYL THIOESTER REDUCTASE


Mass: 39555.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA TROPICALIS (yeast) / Strain: PK233 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): BJ1991
References: UniProt: Q8WZM3, EC: 1.3.1.10, trans-2-enoyl-CoA reductase (NADPH)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 3.5 Å3/Da / Density % sol: 64.83 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15.7 mg/mlprotein1drop
250 mMsodium phosphate1droppH7.0
3150 mM1dropNaCl
42.0 Mammonium sulfate1reservoir
50.1 MADA/NaOH1reservoirpH6.5
60.1 M1reservoirMgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54
DetectorType: MARRESEARCH
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. obs: 53552 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.013 / Net I/σ(I): 16.3
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 4.8 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 25 Å / Rmerge(I) obs: 0.013
Reflection shell
*PLUS
% possible obs: 99.2 % / Num. unique obs: 5181 / Rmerge(I) obs: 0.402

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GU7

1gu7


Resolution: 2.25→24.07 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 212740.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2573 5 %RANDOM
Rwork0.178 ---
obs0.178 51164 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.3333 Å2 / ksol: 0.36995 e/Å3
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å22.93 Å20 Å2
2--1.58 Å20 Å2
3----3.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.25→24.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 166 593 6335
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.25→2.33 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.242 258 5.5 %
Rwork0.189 4471 -
obs--90.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NDP_XPLOR_PAR.TXTNDP_XPLOR_TOP.TXT
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5GOL_XPLOR_PAR.TXTGOL_XPLOR_TOP.TXT
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.28

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