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- PDB-4m29: Structure of a GH39 Beta-xylosidase from Caulobacter crescentus -

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Basic information

Entry
Database: PDB / ID: 4m29
TitleStructure of a GH39 Beta-xylosidase from Caulobacter crescentus
ComponentsBeta-xylosidase
KeywordsHYDROLASE / family GH39 / beta-xylosidase
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 ...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 crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPolo, C.C. / Santos, C.R. / Correa, J.M. / Simao, R.C.G. / Seixas, F.A.V. / Murakami, M.T.
CitationJournal: Thesis
Title: Structure of a GH39 Beta-xylosidase from Caulobacter crescentus
Authors: Polo, C.C. / Santos, C.R. / Correa, J.M. / Simao, R.C.G. / Seixas, F.A.V. / Murakami, M.T.
History
DepositionAug 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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

Downloads & links

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Assembly

Deposited unit
A: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5012
Polymers56,3061
Non-polymers1951
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.287, 57.347, 94.050
Angle α, β, γ (deg.)90.00, 91.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-xylosidase


Mass: 56305.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: ATCC 19089 / CB15 / Gene: Itgav, CC_2357 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A5U0
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.02 Å3/Da / Density % sol: 39.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES, 12% PEG6000, 0.05 M NaCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.6 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 5, 2012
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 2.1→17.4 Å / Num. all: 25413 / Num. obs: 25082 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1
Reflection shellResolution: 2.1→2.14 Å / % possible all: 96.8

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Processing

Software
NameVersionClassification
NatXraydata collection
PHASERphasing
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4EKJ

4ekj


Resolution: 2.1→17.4 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.846 / SU B: 11.983 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1288 5.1 %RANDOM
Rwork0.228 ---
obs0.231 24125 96.04 %-
all-25082 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å2-0.15 Å2
2---2.05 Å2-0 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.1→17.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 12 149 3719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193663
X-RAY DIFFRACTIONr_bond_other_d0.0020.023452
X-RAY DIFFRACTIONr_angle_refined_deg1.91.9544978
X-RAY DIFFRACTIONr_angle_other_deg1.00737919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1695438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23922.816174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28115585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5381531
X-RAY DIFFRACTIONr_chiral_restr0.1220.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214095
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02876
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 99 -
Rwork0.264 1738 -
obs--95.33 %
Refinement TLS params.Method: refined / Origin x: -10.2259 Å / Origin y: -3.0899 Å / Origin z: -23.8065 Å
111213212223313233
T0.0199 Å2-0.003 Å2-0.0078 Å2-0.0543 Å20.0032 Å2--0.0045 Å2
L0.0733 °20.0272 °20.1196 °2-0.3909 °2-0.1111 °2--0.312 °2
S0.0192 Å °0.0106 Å °-0.0051 Å °-0.0176 Å °-0.0024 Å °-0.0019 Å °0.045 Å °-0.0063 Å °-0.0168 Å °

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