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- PDB-1qoz: Catalytic core domain of acetyl xylan esterase from Trichoderma reesei -

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Basic information

Entry
Database: PDB / ID: 1qoz
TitleCatalytic core domain of acetyl xylan esterase from Trichoderma reesei
ComponentsACETYL XYLAN ESTERASE
KeywordsHYDROLASE / ESTERASE / XYLAN DEGRADATION
Function / homology
Function and homology information


acetylxylan esterase / acetylxylan esterase activity / cellulose binding / xylan catabolic process / cellulose catabolic process / extracellular region
Similarity search - Function
Cutinase / Cutinase/acetylxylan esterase / Cutinase / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Lipases, serine active site. ...Cutinase / Cutinase/acetylxylan esterase / Cutinase / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Lipases, serine active site. / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetylxylan esterase
Similarity search - Component
Biological speciesTRICHODERMA REESEI (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHakulinen, N. / Rouvinen, J.
Citation
Journal: J.Struct.Biol. / Year: 2000
Title: Three-Dimensional Structure of the Catalytic Core of Acetylxylan Esterase from Trichoderma Reesei: Insights Into the Deacetylation Mechanism
Authors: Hakulinen, N. / Tenkanen, M. / Rouvinen, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Catalytic Core of Acetylxylan Esterase from Trichoderma Reesei
Authors: Hakulinen, N. / Tenkanen, M. / Rouvinen, J.
History
DepositionNov 25, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 2.0Mar 11, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_database_status / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYL XYLAN ESTERASE
B: ACETYL XYLAN ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4614
Polymers42,0182
Non-polymers4422
Water7,656425
1
A: ACETYL XYLAN ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2302
Polymers21,0091
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ACETYL XYLAN ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2302
Polymers21,0091
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.300, 61.000, 40.000
Angle α, β, γ (deg.)107.70, 113.50, 98.80
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6846, 0.2911, -0.6682), (0.2938, -0.7288, -0.6185), (-0.667, -0.6198, 0.4134)
Vector: 22.2721, 27.3855, -1.2862)

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Components

#1: Protein ACETYL XYLAN ESTERASE / AXE


Mass: 21009.152 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-238 / Source method: isolated from a natural source / Source: (natural) TRICHODERMA REESEI (fungus) / Strain: RUTC-30 / References: UniProt: Q99034, acetylxylan esterase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growpH: 8.2
Details: 1.1 M POTASSIUM/SODIUM TARTRATE, 0.1 M TES, 9 MM TRITON-X, PH 8.2
Crystal
*PLUS
Density % sol: 45 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 8.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 mMTriton X-100 solution1drop
25 mg/mlprotein1droppH5.0
40.28 Mpotassium/sodium tartrate1drop
50.025 MTES1drop
61.1 Mpotassium/sodium tartrate1reservoir
70.1 MTES1reservoirpH8.2
3sodium acetate1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 15, 1998
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→99 Å / Num. obs: 27058 / % possible obs: 87 % / Redundancy: 2.07 % / Biso Wilson estimate: 18.76 Å2 / Rsym value: 0.057 / Net I/σ(I): 14.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.38 / Rsym value: 0.247 / % possible all: 46.5
Reflection
*PLUS
% possible obs: 87 % / Num. measured all: 55958 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 47 % / Rmerge(I) obs: 0.247

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BS9

1bs9


Resolution: 1.9→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2552 10 %RANDOM
Rwork0.186 ---
obs0.186 25039 87 %-
Displacement parametersBiso mean: 15.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 28 425 3390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.197
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.65
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.055
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.32 131 10 %
Rwork0.279 1353 -
obs--46.5 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.65
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.055
LS refinement shell
*PLUS
Rfactor Rfree: 0.32

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