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- PDB-4hkl: Crystal Structures of Mutant Endo-beta-1,4-xylanase II Complexed ... -

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Basic information

Entry
Database: PDB / ID: 4hkl
TitleCrystal Structures of Mutant Endo-beta-1,4-xylanase II Complexed with substrate (1.15 A) and Products (1.6 A)
ComponentsEndo-1,4-beta-xylanase 2Xylanase
KeywordsHYDROLASE / xylanase II / xylohexaose / xylotriose / induced fit mechanism / oxocarbenium ion
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
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
IODIDE ION / Endo-1,4-beta-xylanase 2
Similarity search - Component
Biological speciesTrichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsLangan, P. / Wan, Q. / Coates, L. / Kovalevsky, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism.
Authors: Wan, Q. / Zhang, Q. / Hamilton-Brehm, S. / Weiss, K. / Mustyakimov, M. / Coates, L. / Langan, P. / Graham, D. / Kovalevsky, A.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2595
Polymers20,7511
Non-polymers5084
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.307, 59.032, 69.717
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Endo-1,4-beta-xylanase 2 / Xylanase / Xylanase 2 / 1 / 4-beta-D-xylan xylanohydrolase 2


Mass: 20751.381 Da / Num. of mol.: 1 / Mutation: N76H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma reesei (fungus) / Gene: xyn2 / Plasmid: pJexpress401 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36217, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 15-20 % PEG 8,000, 0.2 M NaI, 0.1 M MES, pH6.0 , pH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.1→15 Å / Num. obs: 81313 / % possible obs: 99.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.051 / Χ2: 1.02 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.1-1.123.70.62939470.914198.6
1.12-1.143.90.54240030.941199.6
1.14-1.164.10.46240270.963199.7
1.16-1.184.20.39239840.989199.9
1.18-1.214.20.3640461.0021100
1.21-1.244.30.32540231.0061100
1.24-1.274.30.2840600.9911100
1.27-1.34.30.24140321.0091100
1.3-1.344.30.21240480.9881100
1.34-1.394.30.17940300.9921100
1.39-1.444.40.14840480.9591100
1.44-1.494.30.11940380.991100
1.49-1.564.40.09640611.045199.9
1.56-1.644.40.08540731.187199.9
1.64-1.754.40.08440691.2541100
1.75-1.884.40.07240761.114199.9
1.88-2.074.30.0541040.791199.9
2.07-2.374.30.03341320.8071100
2.37-2.984.40.02441691.211100
2.98-154.20.0243431.186199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→15 Å / Occupancy max: 1 / Occupancy min: 0.14 / FOM work R set: 0.9465 / SU ML: 0.08 / σ(F): 1.34 / Phase error: 10.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1289 4108 5.06 %
Rwork0.1192 --
obs0.1197 81236 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 36.07 Å2 / Biso mean: 12.8405 Å2 / Biso min: 6.31 Å2
Refinement stepCycle: LAST / Resolution: 1.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1474 0 4 261 1739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071593
X-RAY DIFFRACTIONf_angle_d1.3152195
X-RAY DIFFRACTIONf_chiral_restr0.084221
X-RAY DIFFRACTIONf_plane_restr0.007291
X-RAY DIFFRACTIONf_dihedral_angle_d12.539558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1002-1.11310.25911310.23322529266096
1.1131-1.12670.23751540.20592600275499
1.1267-1.14090.20261320.183626222754100
1.1409-1.15590.18341510.162426432794100
1.1559-1.17180.16731410.141626072748100
1.1718-1.18850.15311470.142926172764100
1.1885-1.20620.16681360.135826742810100
1.2062-1.22510.16051330.133926092742100
1.2251-1.24510.15211460.130426432789100
1.2451-1.26660.15691390.123226502789100
1.2666-1.28960.12981370.109526412778100
1.2896-1.31440.11621130.103726722785100
1.3144-1.34120.13051530.099726682821100
1.3412-1.37040.10361330.095226392772100
1.3704-1.40220.11211500.090226092759100
1.4022-1.43730.10181440.085326622806100
1.4373-1.47610.09431380.085226812819100
1.4761-1.51950.10241370.084826402777100
1.5195-1.56850.09751490.083626562805100
1.5685-1.62450.09621440.081926532797100
1.6245-1.68940.11091530.090326512804100
1.6894-1.76620.12921540.095326572811100
1.7662-1.85920.09611420.093626812823100
1.8592-1.97540.11641160.099227002816100
1.9754-2.12750.10951520.096526892841100
2.1275-2.34090.10311550.106426902845100
2.3409-2.6780.12021420.118827252867100
2.678-3.36770.13121380.123527582896100
3.3677-15.00940.15811480.16982862301099

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