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- PDB-2axe: IODINATED COMPLEX OF ACETYL XYLAN ESTERASE AT 1.80 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 2axe
TitleIODINATED COMPLEX OF ACETYL XYLAN ESTERASE AT 1.80 ANGSTROMS
ComponentsACETYL XYLAN ESTERASE
KeywordsHYDROLASE / IODOTYROSINES / ESTERASE
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 / SIRAS / Resolution: 1.8 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 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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)21,2612
Polymers21,1651
Non-polymers961
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.900, 61.278, 72.538
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: 21165.391 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.: 91 / 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: 1.6 Å3/Da / Density % sol: 22.9 %
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: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorDetector: IMAGE PLATE / Date: Dec 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→99 Å / Num. obs: 15046 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.11
Reflection shellResolution: 1.8→1.9 Å / Mean I/σ(I) obs: 2 / % possible all: 99
Reflection
*PLUS
Num. measured all: 99865

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Processing

Software
NameClassification
DENZOdata reduction
SHELXmodel building
SHELXrefinement
SHELXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→99 Å / Num. parameters: 6189 / Num. restraintsaints: 6009 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: C-I BONDS WERE NOT RESTRAINED
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 763 5.1 %RANDOM
all0.1733 15003 --
obs0.1768 -99.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 1182 / Occupancy sum non hydrogen: 1540.2
Refinement stepCycle: LAST / Resolution: 1.8→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 33 91 1546
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.057
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.173 / Rfactor Rwork: 0.1768
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg26.801
X-RAY DIFFRACTIONs_plane_restr1.209

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