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- PDB-1bs9: ACETYLXYLAN ESTERASE FROM P. PURPUROGENUM REFINED AT 1.10 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 1bs9
TitleACETYLXYLAN ESTERASE FROM P. PURPUROGENUM REFINED AT 1.10 ANGSTROMS
ComponentsACETYL XYLAN ESTERASE
KeywordsSERINE HYDROLASE / ESTERASE / ALPHA/BETA HYDROLASE
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 / SIRAS / Resolution: 1.1 Å
AuthorsGhosh, D. / Erman, M. / Sawicki, M.W. / Lala, P. / Weeks, D.R. / Li, N. / Pangborn, W. / Thiel, D.J. / Jornvall, H. / Eyzaguirre, J.
CitationJournal: 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.
History
DepositionSep 1, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYL XYLAN ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7582
Polymers20,6621
Non-polymers961
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.886, 60.983, 72.425
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


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


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


Mass: 18.015 Da / Num. of mol.: 143 / 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: 1.57 Å3/Da / Density % sol: 22 %
Crystal growpH: 6 / Details: pH 6.0
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.3 / 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: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.92
DetectorType: PRINCETON 2K / Detector: CCD / Date: Feb 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.1→99 Å / Num. obs: 44040 / % possible obs: 69.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 32
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4 / % possible all: 45
Reflection
*PLUS
Num. measured all: 149250
Reflection shell
*PLUS
% possible obs: 44.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SHELXmodel building
SHELXrefinement
SHELXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.1→99 Å / Num. parameters: 14389 / Num. restraintsaints: 16950 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 2232 5.1 %RANDOM
all0.1226 43972 --
obs0.1279 -69.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 1203 / Occupancy sum non hydrogen: 1576.5
Refinement stepCycle: LAST / Resolution: 1.1→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 5 143 1598
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.091
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.063
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 44020 / Rfactor Rwork: 0.1279
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg25.978
X-RAY DIFFRACTIONs_plane_restr1.465

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