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- PDB-1i1w: 0.89A Ultra high resolution structure of a Thermostable Xylanase ... -

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Basic information

Entry
Database: PDB / ID: 1i1w
Title0.89A Ultra high resolution structure of a Thermostable Xylanase from Thermoascus Aurantiacus
ComponentsENDO-1,4-BETA-XYLANASE
KeywordsHYDROLASE / XYLAN DEGRADATION / GLYCOSIDASE / ENZYME / ULTRA HIGH RESOLUTION / CRYO TEMPERATURE / 1 / 4-BETA-XYLAN XYLANOHYDROLASE
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / 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
ACETONE / ETHANOL / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesThermoascus aurantiacus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.89 Å
AuthorsNatesh, R. / Ramakumar, S. / Viswamitra, M.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Thermostable xylanase from Thermoascus aurantiacus at ultrahigh resolution (0.89 A) at 100 K and atomic resolution (1.11 A) at 293 K refined anisotropically to small-molecule accuracy.
Authors: Natesh, R. / Manikandan, K. / Bhanumoorthy, P. / Viswamitra, M.A. / Ramakumar, S.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal Structure at 1.8 A Resolution and Proposed Amino Acid Sequence of a Thermostable Xylanase from Thermoascus Aurantiascus
Authors: Natesh, R. / Bhanumoorthy, P. / Vithayathil, P.J. / Sekar, K. / Ramakumar, S. / Viswamitra, M.A.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Crystals of Thermoascus Aurantiacus Xylanase
Authors: Viswamitra, M.A. / Bhanumoorthy, P. / Ramakumar, S. / Manjula, M.V. / Vithayathil, P.J. / Murthy, S.K. / Naren, A.P.
History
DepositionFeb 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Jun 4, 2014Group: Non-polymer description
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,57223
Polymers32,8691
Non-polymers70322
Water7,458414
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.050, 66.990, 50.760
Angle α, β, γ (deg.)90.00, 113.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 32868.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermoascus aurantiacus (fungus) / Strain: STRAIN ISOLATED FROM LOCAL INDIAN SOIL / References: UniProt: P23360, endo-1,4-beta-xylanase

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Non-polymers , 5 types, 436 molecules

#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#5: Chemical ChemComp-ACN / ACETONE


Mass: 58.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.95 Å3/Da / Density % sol: 36.81 %
Description: STARTING MODEL WAS LOCALLY AVAILABLE INTERMEDIATE REFINED 1.11 A ROOM TEMPERATURE MODEL. THE STRANGE HETERO MOLECULES SEEN IN 0.89 A HIGH RESOLUTION MAPS, labelled as "UNX 1406 TO UNX ...Description: STARTING MODEL WAS LOCALLY AVAILABLE INTERMEDIATE REFINED 1.11 A ROOM TEMPERATURE MODEL. THE STRANGE HETERO MOLECULES SEEN IN 0.89 A HIGH RESOLUTION MAPS, labelled as "UNX 1406 TO UNX 1410" and "UNX 1411 TO UNX 1418", ARE YET TO BE IDENTIFIED. EOH AND ACN WERE ASSIGNED BASED ON UNRESTRAINED BOND LENGTH AND ANGLES.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: Ammonium Sulphate, TRIS/HCl, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Viswamitra, M.A., (1993) J.Mol.Biol., 232, 987.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %protein1drop
210 %(w/v)PEG60001drop
350 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 1999 / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 0.89→35 Å / Num. obs: 177476 / % possible obs: 92 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 32.65
Reflection shellResolution: 0.89→0.92 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 7.82 / % possible all: 83
Reflection
*PLUS
Lowest resolution: 35 Å / % possible obs: 92 % / Redundancy: 4.8 % / Num. measured all: 858643
Reflection shell
*PLUS
% possible obs: 83 % / Rmerge(I) obs: 0.18

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Processing

Software
NameVersionClassification
HKL-2000SUITEdata collection
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LOCALLY AVAILABLE INTERMEDIATE REFINED ROOM TEMP. 1.11 A MODEL

Resolution: 0.89→10 Å / Num. parameters: 24867 / Num. restraintsaints: 1 / Cross valid method: FREE R / σ(F): 0
StereochEM target val spec case: FINAL 18 CYCLES OF BLOCKED L.S. REFINEMENT (2 CYCLES ON EACH OF 9 BLOCKS) WAS PERFORMED USING SHELXL WITHOUT ANY RESTRAINS.
Stereochemistry target values: ENGH AND HUBER
Details: AS THE MOLECULE WAS REFINED WITH NO RESTRAINTS THE NON PLANARITY OF THE ARG 124 B CONFORMER AMIDE GROUP MAY NOT BE TAKEN AS TRUE SINCE THE PLANARITY RESTRAINTS WERE NOT IMPOSED TO THIS ...Details: AS THE MOLECULE WAS REFINED WITH NO RESTRAINTS THE NON PLANARITY OF THE ARG 124 B CONFORMER AMIDE GROUP MAY NOT BE TAKEN AS TRUE SINCE THE PLANARITY RESTRAINTS WERE NOT IMPOSED TO THIS SPARCINGLY OCCUPIED DISORDERED ALTERNATE CONFORMER B. CNS 0.4 was also used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.1061 1766 1 %RANDOM
Rwork0.09 ---
all-174690 --
obs--90.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-
Refine analyzeNum. disordered residues: 51 / Occupancy sum hydrogen: 2125 / Occupancy sum non hydrogen: 2765.87
Refinement stepCycle: LAST / Resolution: 0.89→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 59 414 2792
LS refinement shellResolution: 0.89→0.92 Å
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rwork: 0.09
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.036
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.54
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg23.86
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg2.83

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