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- PDB-4ekj: Crystal structure of a monomeric beta-xylosidase from Caulobacter... -

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Basic information

Entry
Database: PDB / ID: 4ekj
TitleCrystal structure of a monomeric beta-xylosidase from Caulobacter crescentus CB15
ComponentsBeta-xylosidaseXylan 1,4-b-xylosidase
KeywordsHYDROLASE / TIM-barrel fold / hemicellulase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolase domain; family 39 / : / : / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Glycosyl hydrolase domain; family 39 / : / : / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSantos, C.R. / Polo, C.C. / Correa, J.M. / Simao, R.C.G. / Seixas, F.A.V. / Murakami, M.T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The accessory domain changes the accessibility and molecular topography of the catalytic interface in monomeric GH39 beta-xylosidases.
Authors: Santos, C.R. / Polo, C.C. / Correa, J.M. / Simao, R.C. / Seixas, F.A. / Murakami, M.T.
History
DepositionApr 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7866
Polymers56,3061
Non-polymers4805
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.185, 71.185, 226.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-895-

HOH

21A-921-

HOH

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Components

#1: Protein Beta-xylosidase / Xylan 1,4-b-xylosidase


Mass: 56305.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: Itgav, CC_2357 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A5U0, xylan 1,4-beta-xylosidase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulphate cobalt chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.46 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 11, 2011
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 2.5→24.7 Å / Num. all: 36730 / Num. obs: 20621 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.5→2.59 Å / % possible all: 97.2

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Processing

Software
NameVersionClassification
NatXraydata collection
PHASERphasing
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W91

1w91


Resolution: 2.5→24.7 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.33 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24816 1035 5.1 %RANDOM
Rwork0.18832 ---
all0.221 20250 --
obs0.1913 19215 95.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.413 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3942 0 25 235 4202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224076
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.9615549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7915494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21323.005193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.95915653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.181534
X-RAY DIFFRACTIONr_chiral_restr0.0890.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213150
X-RAY DIFFRACTIONr_mcbond_it0.4291.52464
X-RAY DIFFRACTIONr_mcangle_it0.79923984
X-RAY DIFFRACTIONr_scbond_it1.12231612
X-RAY DIFFRACTIONr_scangle_it1.8864.51564
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.184 78 -
Rwork0.122 1353 -
obs--94.39 %

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