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- PDB-1eqp: EXO-B-(1,3)-GLUCANASE FROM CANDIDA ALBICANS -

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Basic information

Entry
Database: PDB / ID: 1eqp
TitleEXO-B-(1,3)-GLUCANASE FROM CANDIDA ALBICANS
ComponentsEXO-B-(1,3)-GLUCANASE
KeywordsHYDROLASE / CANDIDA ALBICANS / EXOGLUCANASE / ALTERNATIVE CODON USAGE
Function / homology
Function and homology information


glucan metabolic process / single-species biofilm formation in or on host organism / glucan 1,3-beta-glucosidase / glucan exo-1,3-beta-glucosidase activity / single-species biofilm formation on inanimate substrate / glucan catabolic process / fungal-type cell wall organization / Transferases; Glycosyltransferases; Hexosyltransferases / cell-substrate adhesion / cell adhesion molecule binding ...glucan metabolic process / single-species biofilm formation in or on host organism / glucan 1,3-beta-glucosidase / glucan exo-1,3-beta-glucosidase activity / single-species biofilm formation on inanimate substrate / glucan catabolic process / fungal-type cell wall organization / 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: 1.9 Å
AuthorsCutfield, J.F. / Sullivan, P.A. / Cutfield, S.M.
Citation
Journal: Protein Eng. / Year: 2000
Title: Minor structural consequences of alternative CUG codon usage (Ser for Leu) in Candida albicans exoglucanase.
Authors: Cutfield, J.F. / Sullivan, P.A. / Cutfield, S.M.
#1: Journal: 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
DepositionApr 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,2441
Polymers45,2441
Non-polymers00
Water5,080282
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.10, 65.30, 96.40
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 EXO-B-(1,3)-GLUCANASE


Mass: 45243.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / Strain: ATCC10261 / References: UniProt: P29717, glucan 1,3-beta-glucosidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: HEPES BUFFER, CACL2, PEG 8000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Details: Chambers, R.S., (1993) J. Gen. Microbiol., 139, 325., Chambers, R.S., (1993) FEBS Lett., 327, 366.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 12, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→54 Å / Num. all: 29591 / Num. obs: 26304 / % possible obs: 90.3 % / Observed criterion σ(F): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 14.2
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.103 / % possible all: 48.7
Reflection
*PLUS
Highest resolution: 1.9 Å
Reflection shell
*PLUS
% possible obs: 56.6 % / Mean I/σ(I) obs: 7

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Processing

Software
NameVersionClassification
ROTAVATAdata reduction
REFMACrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.195 1086 same set as 1CZ1
Rwork0.156 --
all0.154 29282 -
obs0.154 25186 -
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 0 282 3507
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.025
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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