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- PDB-1gyr: Mutant form of enoyl thioester reductase from Candida tropicalis -

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Basic information

Entry
Database: PDB / ID: 1gyr
TitleMutant form of enoyl thioester reductase from Candida tropicalis
Components2,4-DIENOYL-COA REDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADPH) / enoyl-[acyl-carrier-protein] 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 / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily ...: / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / 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
Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial
Similarity search - Component
Biological speciesCANDIDA TROPICALIS (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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
DepositionApr 29, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,39723
Polymers118,5193
Non-polymers1,87820
Water2,990166
1
A: 2,4-DIENOYL-COA REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0717
Polymers39,5061
Non-polymers5646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 2,4-DIENOYL-COA REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1638
Polymers39,5061
Non-polymers6577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: 2,4-DIENOYL-COA REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1638
Polymers39,5061
Non-polymers6577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)156.015, 104.139, 93.952
Angle α, β, γ (deg.)90.00, 99.77, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.38, -0.924, 0.039), (0.925, -0.378, 0.05), (-0.032, 0.055, 0.998)25.5899, 58.91285, 0.90626
2given(-0.747, 0.662, 0.054), (-0.661, -0.749, 0.037), (0.065, -0.009, 0.998)60.53814, 98.59795, -1.67732
DetailsCHAINS A AND B FORM A CLOSE CONTACT IN THE CRYSTAL, VIA BETA SHEET INTERACTIONS BETWEEN STRAND AD OF CHAIN A AND STRAND AD OF CHAIN B . CHAIN C FORMS SIMILAR INTERACTIONS WITH ANOTHER CRYSTAL-SYMMETRY RELATED CHAIN.

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Components

#1: Protein 2,4-DIENOYL-COA REDUCTASE / 2-ENOYL THIOESTER REDUCTASE


Mass: 39506.332 Da / Num. of mol.: 3 / Mutation: YES
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
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION TYR 79 ASN, CHAINS A,B AND C

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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: 3.17 Å3/Da / Density % sol: 61.24 %
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-IDDetails
11.9 Mammonium sulfate1reservoir
20.1 MADA/NaOH1reservoirpH7.0
315 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 44923 / % possible obs: 98.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.9
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 6.9 / % possible all: 90.3
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Lowest resolution: 2.69 Å / % possible obs: 90.3 % / Num. unique obs: 4364

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Processing

Software
NameClassification
REFMACrefinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GU7

1gu7


Resolution: 2.6→19.96 Å / SU B: 10.347 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.527 / ESU R Free: 0.294 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24595 2247 5 %RANDOM
Rwork0.19274 ---
obs0.19539 42676 99.1 %-
Displacement parametersBiso mean: 27.948 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.34 Å2
2--0.4 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8352 0 111 166 8629
Refinement
*PLUS
Num. reflection obs: 44923 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.061
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.6

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