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- PDB-1n9g: Mitochondrial 2-enoyl thioester reductase Etr1p/Etr2p heterodimer... -

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Basic information

Entry
Database: PDB / ID: 1n9g
TitleMitochondrial 2-enoyl thioester reductase Etr1p/Etr2p heterodimer from Candida tropicalis
Components(2,4-dienoyl-CoA reductase) x 2
KeywordsHYDROLASE / heterodimer / Rossmann fold
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial / Enoyl-[acyl-carrier-protein] reductase 2, mitochondrial
Similarity search - Component
Biological speciesCandida tropicalis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsTorkko, J.M. / Koivuranta, K.T. / Kastaniotis, A.J. / Airenne, T.T. / Glumoff, T. / Ilves, M. / Hartig, A. / Gurvitz, A. / Hiltunen, J.K.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Candida tropicalis expresses two mitochondrial 2-enoyl thioester reductases that are able to form both homodimers and heterodimers.
Authors: Torkko, J.M. / Koivuranta, K.T. / Kastaniotis, A.J. / Airenne, T.T. / Glumoff, T. / Ilves, M. / Hartig, A. / Gurvitz, A. / Hiltunen, J.K.
History
DepositionNov 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Derived calculations / Structure summary / Category: pdbx_entry_details / struct_conn

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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
E: 2,4-dienoyl-CoA reductase
F: 2,4-dienoyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,98616
Polymers253,0836
Non-polymers2,90310
Water27,3831520
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)229.453, 95.501, 164.229
Angle α, β, γ (deg.)90.00, 124.71, 90.00
Int Tables number5
Space group name H-MC121
DetailsThere are six chains in the asymmetric unit, three of which are Etr1p protein and three are Etr2p protein. The chains form all three possible dimers: Etr1p/Etr1p homodimer, Etr2p/Etr2p homodimer and Etr1p/Etr2p heterodimer. In each dimer one chain binds NADPH and one not.

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Components

#1: Protein 2,4-dienoyl-CoA reductase


Mass: 42158.516 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tropicalis (yeast) / Gene: ETR2 / Plasmid: pYE352::ETR2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): ybr026c[delta] / References: UniProt: Q8WZM4
#2: Protein 2,4-dienoyl-CoA reductase


Mass: 42202.531 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tropicalis (yeast) / Gene: ETR1 / Plasmid: pYE352::ETR1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): ybr026c[delta] / References: UniProt: Q8WZM3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1520 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, ADA/NaOH, NADPH, octanoyl-CoA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
21.8 Mammonium sulfate1reservoir
30.1 MADA1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.076 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.076 Å / Relative weight: 1
ReflectionHighest resolution: 1.98 Å / Num. obs: 212894 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.98→2.086 Å
Reflection
*PLUS
Lowest resolution: 19.43 Å / % possible obs: 97.5 % / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 95.2 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GU7

1gu7


Resolution: 1.98→19.43 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23483 10101 -random
Rwork0.19534 ---
all0.19731 ---
obs0.19731 191906 99.81 %-
Refinement stepCycle: LAST / Resolution: 1.98→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16718 0 179 1520 18417
Refinement
*PLUS
Num. reflection obs: 202400 / Num. reflection Rfree: 10494 / Rfactor Rfree: 0.2348 / Rfactor Rwork: 0.1953
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.013
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.46

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