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- PDB-3vsv: The complex structure of XylC with xylose -

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Basic information

Entry
Database: PDB / ID: 3vsv
TitleThe complex structure of XylC with xylose
ComponentsXylosidase
KeywordsHYDROLASE / glycoside hydrolase / beta-xylosidase / product inhibition
Function / homology
Function and homology information


carbon-oxygen lyase activity, acting on polysaccharides / extracellular region
Similarity search - Function
: / Glycoside hydrolase 120, insertion domain / : / Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold ...: / Glycoside hydrolase 120, insertion domain / : / Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-xylopyranose / alpha-D-xylopyranose / Parallel beta-helix repeat protein
Similarity search - Component
Biological speciesThermoanaerobacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsHuang, C.H. / Sun, Y. / Ko, T.P. / Ma, Y. / Chen, C.C. / Zheng, Y. / Chan, H.C. / Pang, X. / Wiegel, J. / Shao, W. / Guo, R.T.
CitationJournal: Biochem.J. / Year: 2012
Title: The substrate/product-binding modes of a novel GH120 beta-xylosidase (XylC) from Thermoanaerobacterium saccharolyticum JW/SL-YS485
Authors: Huang, C.H. / Sun, Y. / Ko, T.P. / Chen, C.C. / Zheng, Y. / Chan, H.C. / Pang, X. / Wiegel, J. / Shao, W. / Guo, R.T.
History
DepositionMay 9, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_validate_close_contact / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xylosidase
B: Xylosidase
C: Xylosidase
D: Xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,63639
Polymers291,3824
Non-polymers5,25535
Water65,0883613
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24530 Å2
ΔGint-105 kcal/mol
Surface area83420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.779, 201.948, 100.105
Angle α, β, γ (deg.)90.00, 99.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Xylosidase / beta-xylosidase


Mass: 72845.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium (bacteria) / Strain: JW/SL YS485 / Plasmid: pHsh / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: A2ICH1, xylan 1,4-beta-xylosidase
#2: Sugar...
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3613 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M sodium citrate, 15-17%(w/v) polyethylene glycol 3350, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorDate: Mar 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→25 Å / Num. obs: 574432 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.9
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.3 / Num. unique all: 57397 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VST

3vst


Resolution: 1.48→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.168 27272 RANDOM
Rwork0.15 --
all-575333 -
obs-548128 -
Refinement stepCycle: LAST / Resolution: 1.48→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20588 0 350 3613 24551
LS refinement shellResolution: 1.48→1.53 Å
RfactorNum. reflection% reflection
Rfree0.228 2468 -
Rwork0.217 --
obs-49577 95.3 %

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