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- PDB-1pvx: DO-1,4-BETA-XYLANASE, ROOM TEMPERATURE, PH 4.5 -

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Basic information

Entry
Database: PDB / ID: 1pvx
TitleDO-1,4-BETA-XYLANASE, ROOM TEMPERATURE, PH 4.5
ComponentsPROTEIN (ENDO-1,4-BETA-XYLANASE)
KeywordsHYDROLASE / THERMOPHILIC / XYLANASE / FAMILY-11 OF GLYCOSYL HYDROLASES
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 ...Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesPaecilomyces variotii (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsRajeshkumar, P. / Eswaramoorthy, S. / Vithayathil, P.J. / Viswamitra, M.A.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The tertiary structure at 1.59 A resolution and the proposed amino acid sequence of a family-11 xylanase from the thermophilic fungus Paecilomyces varioti bainier.
Authors: Kumar, P.R. / Eswaramoorthy, S. / Vithayathil, P.J. / Viswamitra, M.A.
History
DepositionOct 20, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (ENDO-1,4-BETA-XYLANASE)


Theoretical massNumber of molelcules
Total (without water)20,9591
Polymers20,9591
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.762, 54.058, 90.064
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 PROTEIN (ENDO-1,4-BETA-XYLANASE) / XYLA


Mass: 20959.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paecilomyces variotii (fungus) / References: UniProt: P81536, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growpH: 4.5 / Details: pH 4.50

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 3, 1997 / Details: MIRRORS
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.59→20 Å / Num. obs: 24200 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Redundancy: 5.13 % / Biso Wilson estimate: 19.23 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 25.71
Reflection shellResolution: 1.59→1.7 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.19 / % possible all: 78

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Processing

Software
NameVersionClassification
XDSdata scaling
AUTOMARdata reduction
AMoREphasing
X-PLOR3.851refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YNA

1yna


Resolution: 1.59→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE STRUCTURE WAS REFINED USING BOTH X-PLOR AND REFMAC. A BULK SOLVENT CORRECTION WAS USED IN EACH CASE.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2394 10 %RANDOM
Rwork0.191 ---
obs0.191 24200 92.5 %-
Displacement parametersBiso mean: 23.56 Å2
Refinement stepCycle: LAST / Resolution: 1.59→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 0 128 1621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.64
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.17
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
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO

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