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- PDB-2fuk: Crystal structure of XC6422 from Xanthomonas campestris: a member... -

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Basic information

Entry
Database: PDB / ID: 2fuk
TitleCrystal structure of XC6422 from Xanthomonas campestris: a member of a/b serine hydrolase without lid at 1.6 resolution
ComponentsXC6422 protein
KeywordsHYDROLASE / a/b hydrolase / Xanthomonas campestris / structural genomics
Function / homologyXaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Conserved enzyme
Function and homology information
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsYang, C.Y. / Chin, K.H. / Chou, C.C. / Wang, A.H.J. / Chou, S.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Structure of XC6422 from Xanthomonas campestris at 1.6 A resolution: a small serine alpha/beta-hydrolase
Authors: Yang, C.Y. / Chin, K.H. / Chou, C.C. / Wang, A.H.J. / 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: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XC6422 protein


Theoretical massNumber of molelcules
Total (without water)24,0011
Polymers24,0011
Non-polymers00
Water81145
1
A: XC6422 protein

A: XC6422 protein


Theoretical massNumber of molelcules
Total (without water)48,0022
Polymers48,0022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)74.980, 79.490, 38.120
Angle α, β, γ (deg.)90.00, 108.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein XC6422 protein / a member of a/b serine hydrolase


Mass: 24001.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: B0RM26
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 8

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Na cacodylate pH6.5, 1.6M (NH4)2SO4, 2% PEG 400, 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: 0.98977 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 2, 2005
RadiationMonochromator: Se-Met / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98977 Å / Relative weight: 1
ReflectionResolution: 1.6→24.8 Å / Num. all: 27824 / Num. obs: 27545 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 1.6 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→24.8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.24 -Random
Rwork0.21 --
all0.22 27824 -
obs0.22 27545 -
Refinement stepCycle: LAST / Resolution: 1.6→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 0 45 1725

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