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- PDB-1gok: Thermostable xylanase I from Thermoascus aurantiacus- Crystal form II -

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Basic information

Entry
Database: PDB / ID: 1gok
TitleThermostable xylanase I from Thermoascus aurantiacus- Crystal form II
ComponentsENDO-1,4-BETA-XYLANASE
KeywordsHYDROLASE / XYLANASE / FAMILY 10 / PLANT CELL WALL DEGRADATION
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesTHERMOASCUS AURANTIACUS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsLo Leggio, L. / Pickersgill, R.W.
Citation
Journal: FEBS Lett. / Year: 2001
Title: Substrate Specificity and Subsite Mobility in T. Aurantiacus Xylanase 10A
Authors: Lo Leggio, L. / Kalogiannis, S. / Eckert, K. / Teixeira, S.C.M. / Bhat, M.K. / Andrei, C. / Pickersgill, R.W. / Larsen, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Anisotropic Refinement of the Structure of Thermoascus Aurantiacus Xylanase I
Authors: Teixeira, S. / Lo Leggio, L. / Pickersgill, R. / Cardin, C.
#2: Journal: Proteins: Struct.,Funct., Genet. / Year: 1999
Title: High Resolution Structure and Sequence of T. Aurantiacus Xylanase I: Implications for the Evolution of Thermostability in Family 10 Xylanases and Enzymes with Beta/Alpha Barrel Architecture
Authors: Lo Leggio, L. / Kalogiannis, S. / Bhat, M.K. / Pickersgill, R.W.
#3: Journal: Biochem.Soc.Trans. / Year: 1998
Title: Superfamilies: The 4/7 Superfamily of Beta/ Alpha-Barrel Glycosidases and the Right-Handed Parallel Beta-Helix Superfamily
Authors: Pickersgill, R. / Harris, G. / Lo Leggio, L. / Mayans, O. / Jenkins, J.
#4: Journal: Structural Studies of Xylanases and Endoglucanases / Year: 1997
Title: Structure Solution of Thermoascus Aurantiacus Xylanase. Structural Studies of Xylanases and Endoglucanases
Authors: Lo Leggio, L.
History
DepositionOct 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2001Provider: repository / Type: Initial release
SupersessionJun 18, 2002ID: 1TAX
Revision 1.1Sep 4, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Mar 11, 2020Group: Atomic model / Polymer sequence / Category: atom_site / entity_poly
Item: _atom_site.occupancy / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDO-1,4-BETA-XYLANASE


Theoretical massNumber of molelcules
Total (without water)32,8911
Polymers32,8911
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.220, 59.240, 51.310
Angle α, β, γ (deg.)90.00, 109.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE / XYLANASE / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE / TAXI


Mass: 32890.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMOASCUS AURANTIACUS (fungus) / References: UniProt: P23360, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-26 REFER TO THE SIGNAL PEPTIDE. IT IS NOT KNOWN IF GLN 303 IS PRESENT IN THE CRYSTAL

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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: 2.02 Å3/Da / Density % sol: 32.9 % / Description: THE PH OF CRYSTALLIZATION WAS NOT BUFFERED
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROPS CONTAINING 1:1 RATIO OF 20 MG/ML PROTEIN SOLUTION AND RESERVOIR SOLUTION (12 % TO 25 % PEG 6,000)., pH 7.00

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 20, 1995 / Details: MIRRORS
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.14→39.5 Å / Num. obs: 80691 / % possible obs: 85.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.82
Reflection shellResolution: 1.14→1.15 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 3.15 / % possible all: 78.8

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EXO

2exo


Resolution: 1.14→39.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: A VERY IMPORTANT STEP TOWARDS STRUCTURE SOLUTION WAS REFINEMENT USING ARP (AUTOMATED REFINEMENT PROCEDURE)
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2795 3.5 %FREER FLAG (CCP4)
Rwork0.18 ---
obs0.18 80632 85.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.6 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso mean: 13.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.847 Å20 Å2-1.132 Å2
2--0.277 Å20 Å2
3---0.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.1404 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.0939 Å0.0889 Å
Refinement stepCycle: LAST / Resolution: 1.14→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 0 248 2560
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.44
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.7142
X-RAY DIFFRACTIONc_mcangle_it1.0862.5
X-RAY DIFFRACTIONc_scbond_it1.3222.5
X-RAY DIFFRACTIONc_scangle_it2.0443
LS refinement shellResolution: 1.14→1.16 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 133 3.79 %
Rwork0.354 3375 -
obs--75.1 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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