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- PDB-1hv1: DISSECTING ELECTROSTATIC INTERACTIONS AND THE PH-DEPENDENT ACTIVI... -

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Basic information

Entry
Database: PDB / ID: 1hv1
TitleDISSECTING ELECTROSTATIC INTERACTIONS AND THE PH-DEPENDENT ACTIVITY OF A FAMILY 11 GLYCOSIDASE
ComponentsENDO-1,4-BETA-XYLANASE
KeywordsHYDROLASE / beta sheet
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 speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJoshi, M.D. / Sidhu, G. / Nielsen, J.E. / Brayer, G.D. / Withers, S.G. / McIntosh, L.P.
CitationJournal: Biochemistry / Year: 2001
Title: Dissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase.
Authors: Joshi, M.D. / Sidhu, G. / Nielsen, J.E. / Brayer, G.D. / Withers, S.G. / McIntosh, L.P.
History
DepositionJan 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)20,3521
Polymers20,3521
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.994, 52.711, 78.202
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE / E.C.3.2.1.8 / XYLANASE / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE


Mass: 20351.955 Da / Num. of mol.: 1 / Fragment: Q127A_BCX / Mutation: Q127A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Plasmid: PCW / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P09850, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonimu sulphate, sodium chloride, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298 K
Crystal grow
*PLUS
Details: Sidhu, G., (1999) Biochemistry, 38, 5346.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
217 %ammonium sulfate1reservoir
310 mM1reservoirNaCl
440 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 1, 1999
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 17548 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 21.8
Reflection shellResolution: 1.8→1.88 Å / Rmerge(I) obs: 0.115
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 157188
Reflection shell
*PLUS
Mean I/σ(I) obs: 6.6

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Processing

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

1bcx


Resolution: 1.8→10 Å / σ(F): 0
RfactorNum. reflection
Rwork0.164 -
obs0.164 15042
all-15042
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 0 177 1621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg0.911
LS refinement shellResolution: 1.8→10 Å
RfactorNum. reflection% reflection
Rwork0.164 --
obs-15042 95 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Rfactor Rwork: 0.164

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