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- PDB-1afw: THE 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE DIMERIC PEROXISOMAL THI... -

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Basic information

Entry
Database: PDB / ID: 1afw
TitleTHE 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE DIMERIC PEROXISOMAL THIOLASE OF SACCHAROMYCES CEREVISIAE
Components3-KETOACETYL-COA THIOLASE
KeywordsTHIOLASE / FATTY ACID METABOLISM
Function / homology
Function and homology information


alpha-linolenic acid (ALA) metabolism / Beta-oxidation of very long chain fatty acids / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / Peroxisomal protein import / 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 / acetyl-CoA C-acyltransferase activity / Peroxisomal protein import / 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, C-terminal / Thiolase, C-terminal domain / Thiolase ...: / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / 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 / SYNCHROTRON / MIRAS / Resolution: 1.8 Å
AuthorsMathieu, M. / Wierenga, R.K.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism.
Authors: Mathieu, M. / Modis, Y. / Zeelen, J.P. / Engel, C.K. / Abagyan, R.A. / Ahlberg, A. / Rasmussen, B. / Lamzin, V.S. / Kunau, W.H. / Wierenga, R.K.
History
DepositionMar 15, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-KETOACETYL-COA THIOLASE
B: 3-KETOACETYL-COA THIOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3894
Polymers84,1522
Non-polymers2362
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-18 kcal/mol
Surface area25690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.170, 92.650, 116.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9208, 0.3431, 0.1854), (0.3439, 0.4901, 0.801), (0.184, 0.8013, -0.5693)
Vector: 75.093, -77.4854, 112.0084)

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Components

#1: Protein 3-KETOACETYL-COA THIOLASE


Mass: 42076.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: PEROXISOME / Organelle: PEROXISOME / References: UniProt: P27796, acetyl-CoA C-acyltransferase
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.3 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: microdiaylsis / pH: 6.5
Details: MICRODIALYSIS AGAINST 25MM MOPS PH6.5, 200MM DTT, 1MM EDTA, 1MM SODIUM AZIDE, AT 20 DEGREES CELSIUS, microdiaylsis, temperature 293K
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mMMOPS11
21 mMDTT11
31 mM11NaN3
41 mMEDTA11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.995
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.995 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 71570 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 24.8
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 12.4 / % possible all: 86.8

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.8→10 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: R FREE (WITH X-PLOR, BUT NOT WITH TNT) / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3790 5 %EVERY 20TH REFLECTION
Rwork0.203 ---
all0.187 71365 --
obs0.187 71365 98.9 %-
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5874 0 0 464 6338
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01759752.5
X-RAY DIFFRACTIONt_angle_deg2.480471.5
X-RAY DIFFRACTIONt_dihedral_angle_d33.336630
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0091698
X-RAY DIFFRACTIONt_gen_planes0.01186520
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.006189
Software
*PLUS
Name: TNT / Version: 5EA(B) / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0098
X-RAY DIFFRACTIONt_plane_restr0.01120

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