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- PDB-1wzz: Structure of endo-beta-1,4-glucanase CMCax from Acetobacter xylinum -

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Basic information

Entry
Database: PDB / ID: 1wzz
TitleStructure of endo-beta-1,4-glucanase CMCax from Acetobacter xylinum
ComponentsProbable endoglucanase
KeywordsHYDROLASE / Glycoside Hydrolase family 8 (GH-8) / (ALPHA/ALPHA)6 BARREL / Structural Genomics / STRUCTURAL GENOMICS CONSORTIUM for Research on Gene Expression System / SGCGES
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Probable endoglucanase
Similarity search - Component
Biological speciesGluconacetobacter xylinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsYasutake, Y. / Kawano, S. / Tajima, K. / Yao, M. / Satoh, Y. / Munekata, M. / Tanaka, I. / Structural Genomics Consortium (SGC)
CitationJournal: Proteins / Year: 2006
Title: Structural characterization of the Acetobacter xylinum endo-beta-1,4-glucanase CMCax required for cellulose biosynthesis.
Authors: Yasutake, Y. / Kawano, S. / Tajima, K. / Yao, M. / Satoh, Y. / Munekata, M. / Tanaka, I.
History
DepositionMar 10, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5772
Polymers37,4811
Non-polymers961
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.878, 88.878, 93.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Probable endoglucanase / endo-beta-1 / 4-glucanase / Endo-1 / 4-beta- glucanase / Cellulase


Mass: 37480.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconacetobacter xylinus (bacteria) / Gene: cmcAX / Plasmid: pQE3013 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P37696, cellulase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 3 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: PEG 4000, PEG 8000, ammonium sulfate, cellobiose, sodium citrate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. all: 50493 / Num. obs: 50493 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 18.6 Å2 / Rsym value: 0.072 / Net I/σ(I): 28.3
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 5022 / Rsym value: 0.466 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDEphasing
CNSrefinement
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.65→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2507 5 %RANDOM
Rwork0.176 ---
all-50418 --
obs-50418 100 %-
Displacement parametersBiso mean: 21.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.482 Å2-0.978 Å20 Å2
2---1.482 Å20 Å2
3---2.963 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 0 5 312 2808
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01183
X-RAY DIFFRACTIONc_angle_deg1.659
X-RAY DIFFRACTIONc_dihedral_angle_d22.07
X-RAY DIFFRACTIONc_improper_angle_d1.038
LS refinement shellResolution: 1.65→1.71 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.229 248 4.9 %
Rwork0.229 4785 -
obs-5033 100 %

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