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- PDB-2b42: Crystal structure of the Triticum xylanse inhibitor-I in complex ... -

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Basic information

Entry
Database: PDB / ID: 2b42
TitleCrystal structure of the Triticum xylanse inhibitor-I in complex with bacillus subtilis xylanase
Components
  • Endo-1,4-beta-xylanase A
  • xylanase inhibitor-I
KeywordsHYDROLASE INHIBITOR/HYDROLASE / protein-protein complex / two beta-barrel domain / beta-jelly roll / x-ray crystallography / HYDROLASE INHIBITOR-HYDROLASE COMPLEX
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Xylanase inhibitor, C-terminal / Xylanase inhibitor I-like / Xylanase inhibitor C-terminal / Xylanase inhibitor, N-terminal / Xylanase inhibitor N-terminal / 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. ...Xylanase inhibitor, C-terminal / Xylanase inhibitor I-like / Xylanase inhibitor C-terminal / Xylanase inhibitor, N-terminal / Xylanase inhibitor N-terminal / 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 / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Concanavalin A-like lectin/glucanase domain superfamily / Aspartic peptidase domain superfamily / Jelly Rolls / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Endo-1,4-beta-xylanase A / Xylanase inhibitor
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSansen, S. / Dewilde, M. / De Ranter, C.J. / Gebruers, K. / Brijs, K. / Courtin, C.M. / Delcour, J.A. / Rabijns, A.
CitationJournal: Febs J. / Year: 2009
Title: Identification of structural determinants for inhibition strength and specificity of wheat xylanase inhibitors TAXI-IA and TAXI-IIA.
Authors: Pollet, A. / Sansen, S. / Raedschelders, G. / Gebruers, K. / Rabijns, A. / Delcour, J.A. / Courtin, C.M.
History
DepositionSep 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: xylanase inhibitor-I
B: Endo-1,4-beta-xylanase A


Theoretical massNumber of molelcules
Total (without water)59,2562
Polymers59,2562
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-6 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.890, 95.340, 69.310
Angle α, β, γ (deg.)90.00, 122.24, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe asymmmetric unit contains one copy of the protein-protein complex

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Components

#1: Protein xylanase inhibitor-I


Mass: 38846.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: GenBank: 23954367, UniProt: Q8H0K8*PLUS
#2: Protein Endo-1,4-beta-xylanase A / E.C.3.2.1.8 / Xylanase A / 1 / 4- beta-D-xylan xylanohydrolase A


Mass: 20409.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: xynA / Production host: Escherichia coli (E. coli) / References: UniProt: P18429, endo-1,4-beta-xylanase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.6 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.22 M ammonium sulphate, 0.1 M sodium acetate buffer, 25 % (w/v) polyethylene glycol 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 4, 2002
RadiationMonochromator: Sagitally focusing Ge(220) and a multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→29.36 Å / Num. all: 20136 / Num. obs: 18166 / % possible obs: 88.1 % / Observed criterion σ(F): 1.41 / Observed criterion σ(I): 0.7
Reflection shellResolution: 2.5→2.64 Å / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.36 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 9.333 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.731 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23977 1968 9.8 %RANDOM
Rwork0.18265 ---
all0.18814 18166 --
obs0.18814 18166 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.362 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å21.32 Å2
2--0.91 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4047 0 0 65 4112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214163
X-RAY DIFFRACTIONr_bond_other_d0.0020.023675
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9455699
X-RAY DIFFRACTIONr_angle_other_deg0.80838548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1715543
X-RAY DIFFRACTIONr_chiral_restr0.0830.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024713
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02840
X-RAY DIFFRACTIONr_nbd_refined0.2010.2719
X-RAY DIFFRACTIONr_nbd_other0.2420.24070
X-RAY DIFFRACTIONr_nbtor_other0.0830.22487
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.23
X-RAY DIFFRACTIONr_mcbond_it0.6931.52710
X-RAY DIFFRACTIONr_mcangle_it1.28524349
X-RAY DIFFRACTIONr_scbond_it1.45531453
X-RAY DIFFRACTIONr_scangle_it2.4734.51350
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.308 140
Rwork0.256 1376
obs-2965

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