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- PDB-2fuj: A putative acyl-CoA thioesterase from Xanthomonas campestris (XC229) -

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Basic information

Entry
Database: PDB / ID: 2fuj
TitleA putative acyl-CoA thioesterase from Xanthomonas campestris (XC229)
Componentsconserved hypothetical protein
KeywordsHYDROLASE / Xanthomonas campestris / structural genomics / conserved hypothetical protein / hot dog domain / acyl-CoA thioesterase
Function / homology: / Thioesterase-like superfamily / fatty acyl-CoA hydrolase activity / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Thioesterase
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsChin, K.H. / Chou, C.C. / Wang, A.H. / Chou, S.H.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of a putative acyl-CoA thioesterase from Xanthomonas campestris (XC229) adopts a tetrameric hotdog fold of epsilongamma mode.
Authors: Chin, K.H. / Chou, C.C. / Wang, A.H. / Chou, S.H.
History
DepositionJan 27, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)15,1981
Polymers15,1981
Non-polymers00
Water3,081171
1
A: conserved hypothetical protein

A: conserved hypothetical protein

A: conserved hypothetical protein

A: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)60,7934
Polymers60,7934
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area7540 Å2
ΔGint-16 kcal/mol
Surface area23540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)106.590, 106.590, 106.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-144-

HOH

DetailsXC229 was shown to be a homotetramer. However, there was only one subunit per asymmetric unit in the crystals employed in this study. The tetramer was constructed by rotating the contents of the asymmetric unit using the crystallographic I-centered 2-fold symmetry(I23).

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Components

#1: Protein conserved hypothetical protein / XC229 / putative acyl-CoA thioesterase


Mass: 15198.329 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Species: Xanthomonas campestris / Strain: ATCC 33913 / Plasmid: pET20b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8PBH4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: MPD33%, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.9823 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2005
RadiationMonochromator: Se-Met / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9823 Å / Relative weight: 1
ReflectionResolution: 1.7→26.6 Å / Num. all: 43207 / Num. obs: 41911 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→26.6 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.266 250 Random
Rwork0.242 --
all-43207 -
obs-41911 -
Refinement stepCycle: LAST / Resolution: 1.7→26.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 0 171 1106

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