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- PDB-1pxt: THE 2.8 ANGSTROMS STRUCTURE OF PEROXISOMAL 3-KETOACYL-COA THIOLAS... -

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Basic information

Entry
Database: PDB / ID: 1pxt
TitleTHE 2.8 ANGSTROMS STRUCTURE OF PEROXISOMAL 3-KETOACYL-COA THIOLASE OF SACCHAROMYCES CEREVISIAE: A FIVE LAYERED A-B-A-B-A STRUCTURE, CONSTRUCTED FROM TWO CORE DOMAINS OF IDENTICAL TOPOLOGY
ComponentsPEROXISOMAL 3-KETOACYL-COA THIOLASE
KeywordsTHIOLASE
Function / homology
Function and homology information


alpha-linolenic acid (ALA) metabolism / Beta-oxidation of very long chain fatty acids / acetyl-CoA C-acyltransferase / Peroxisomal protein import / acetyl-CoA C-acyltransferase activity / phenylacetate catabolic process / fatty acid beta-oxidation / peroxisomal matrix / Neutrophil degranulation / mitochondrial intermembrane space ...alpha-linolenic acid (ALA) metabolism / Beta-oxidation of very long chain fatty acids / acetyl-CoA C-acyltransferase / Peroxisomal protein import / acetyl-CoA C-acyltransferase activity / phenylacetate catabolic process / fatty acid beta-oxidation / peroxisomal matrix / Neutrophil degranulation / mitochondrial intermembrane space / peroxisome / mRNA binding
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-ketoacyl-CoA thiolase, peroxisomal
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsMathieu, M. / Wierenga, R.K.
CitationJournal: Structure / Year: 1994
Title: The 2.8 A crystal structure of peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: a five-layered alpha beta alpha beta alpha structure constructed from two core domains of identical topology.
Authors: Mathieu, M. / Zeelen, J.P. / Pauptit, R.A. / Erdmann, R. / Kunau, W.H. / Wierenga, R.K.
History
DepositionJul 4, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEROXISOMAL 3-KETOACYL-COA THIOLASE
B: PEROXISOMAL 3-KETOACYL-COA THIOLASE


Theoretical massNumber of molelcules
Total (without water)83,4912
Polymers83,4912
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-21 kcal/mol
Surface area24190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.780, 93.720, 120.450
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 3-KETOACYL-COA THIOLASE


Mass: 41745.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P27796, acetyl-CoA C-acyltransferase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growDetails: THE PROTEIN HAS BEEN CRYSTALLIZED IN THE ABSENCE OF AN ACTIVE SITE LIGAND.
Crystal grow
*PLUS
pH: 7.4 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein11
2200 mMpotasssium phosphate11
31 mMdithiothreitol11
41 mM11NaN3
51 mMEDTA11
625 mMMOPS12
71 mMdithiothreitol12
81 mM12NaN3
91 mMEDTA12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. obs: 18981 / % possible obs: 92 % / Num. measured all: 47231 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 92.6 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→8 Å / σ(F): 0
RfactorNum. reflection
Rfree0.334 -
Rwork0.198 -
obs0.198 18271
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5201 0 0 0 5201
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.198 / Rfactor Rfree: 0.334
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2

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