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- PDB-1g66: ACETYLXYLAN ESTERASE AT 0.90 ANGSTROM RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1g66
TitleACETYLXYLAN ESTERASE AT 0.90 ANGSTROM RESOLUTION
ComponentsACETYL XYLAN ESTERASE II
KeywordsHYDROLASE / serine hydrolase / acetyl xylopyranose / xylan
Function / homology
Function and homology information


acetylxylan esterase / acetylxylan esterase activity / xylan catabolic process / cellulose catabolic process / extracellular region
Similarity search - Function
Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetylxylan esterase 2
Similarity search - Component
Biological speciesPenicillium purpurogenum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.9 Å
AuthorsGhosh, D. / Sawicki, M. / Lala, P. / Erman, M. / Pangborn, W. / Eyzaguirre, J. / Gutierrez, R. / Jornvall, H. / Thiel, D.J.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Multiple conformations of catalytic serine and histidine in acetylxylan esterase at 0.90 A.
Authors: Ghosh, D. / Sawicki, M. / Lala, P. / Erman, M. / Pangborn, W. / Eyzaguirre, J. / Gutierrez, R. / Jornvall, H. / Thiel, D.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Determination of a protein structure by iodination: the structure of iodinated acetylxylan esterase
Authors: Ghosh, D. / Erman, M. / Sawicki, M. / Lala, P. / Weeks, D.R. / Li, N. / Pangborn, W. / Thiel, D.J. / Jornvall, H. / Gutierrez, R. / Eyzaguirre, J.
#2: Journal: Proteins / Year: 1996
Title: Characterization of crystals of P. purpurogenum acetyl xylan esterase from high resolution X-ray diffraction
History
DepositionNov 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYL XYLAN ESTERASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4149
Polymers20,6621
Non-polymers7538
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.541, 59.898, 71.392
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 ACETYL XYLAN ESTERASE II


Mass: 20661.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium purpurogenum (fungus) / References: UniProt: O59893, acetylesterase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.3
Details: Ammonium sulfate, pH 5.3, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Pangborn, W., (1996) Proteons Struct.Funct.Genet., 24, 523.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
250 mMcitrate1drop
313 %satammonium sulfate1drop
433-37 %satammonium sulfate1reservoir
550 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorType: PRINCETON 2K / Detector: CCD / Date: Dec 15, 1995
RadiationMonochromator: Sagitally focussed Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 0.9→99 Å / Num. all: 95283 / Num. obs: 95283 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.41 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 29.2
Reflection shellResolution: 0.9→0.94 Å / Redundancy: 2 % / Rmerge(I) obs: 0.185 / % possible all: 40.4
Reflection
*PLUS
Num. measured all: 420882
Reflection shell
*PLUS
% possible obs: 40.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
SHELXL-97refinement
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.9→99 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.132 4800 RANDOM
Rwork0.107 --
all0.107 95283 -
obs0.107 95283 -
Refine analyzeLuzzati coordinate error obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 0.9→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 44 299 1785
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d1.982
X-RAY DIFFRACTIONs_from_restr_planes1.717
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.103
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg25.23
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.717

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