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- PDB-1cz1: EXO-B-(1,3)-GLUCANASE FROM CANDIDA ALBICANS AT 1.85 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1cz1
TitleEXO-B-(1,3)-GLUCANASE FROM CANDIDA ALBICANS AT 1.85 A RESOLUTION
ComponentsPROTEIN (EXO-B-(1,3)-GLUCANASE)
KeywordsHYDROLASE / EXOGLUCANASE / CANDIDA ALBICANS / GLYCOSIDE HYDROLASE FAMILY 5
Function / homology
Function and homology information


single-species biofilm formation in or on host organism / glucan metabolic process / glucan 1,3-beta-glucosidase / single-species biofilm formation on inanimate substrate / adhesion of symbiont to host cell / glucan exo-1,3-beta-glucosidase activity / fungal-type cell wall organization / glucan catabolic process / Transferases; Glycosyltransferases; Hexosyltransferases / cell-substrate adhesion ...single-species biofilm formation in or on host organism / glucan metabolic process / glucan 1,3-beta-glucosidase / single-species biofilm formation on inanimate substrate / adhesion of symbiont to host cell / glucan exo-1,3-beta-glucosidase activity / fungal-type cell wall organization / glucan catabolic process / Transferases; Glycosyltransferases; Hexosyltransferases / cell-substrate adhesion / cell adhesion molecule binding / extracellular vesicle / transferase activity / cell surface / extracellular region
Similarity search - Function
: / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Glucan 1,3-beta-glucosidase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsCutfield, S.M. / Davies, G.J. / Murshudov, G. / Anderson, B.F. / Moody, P.C.E. / Sullivan, P.A. / Cutfield, J.F.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: The structure of the exo-beta-(1,3)-glucanase from Candida albicans in native and bound forms: relationship between a pocket and groove in family 5 glycosyl hydrolases.
Authors: Cutfield, S.M. / Davies, G.J. / Murshudov, G. / Anderson, B.F. / Moody, P.C. / Sullivan, P.A. / Cutfield, J.F.
History
DepositionSep 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (EXO-B-(1,3)-GLUCANASE)


Theoretical massNumber of molelcules
Total (without water)45,2701
Polymers45,2701
Non-polymers00
Water5,567309
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.790, 64.540, 96.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (EXO-B-(1,3)-GLUCANASE)


Mass: 45269.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Strain: ATCC 10261 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P29717, glucan 1,3-beta-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: Hepes buffer, CaCl2, Peg 8000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal
*PLUS
Density % sol: 35 %
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMHEPES1drop
20.2 M1dropCaCl2
320 %(w/v)PEG80001drop
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→38 Å / Num. all: 96965 / Num. obs: 96965 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.154 / Num. unique all: 3655 / % possible all: 97.5
Reflection
*PLUS
Num. obs: 32353 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 97.5 % / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
MLPHAREphasing
REFMACrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 1.85→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1327 4.3 %random
Rwork0.166 ---
all-31012 --
obs-31012 100 %-
Refinement stepCycle: LAST / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3239 0 0 309 3548
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d0.021
X-RAY DIFFRACTIONp-planar1,4-d0.028
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.3 % / Rfactor obs: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS

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