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- PDB-1ta3: Crystal Structure of xylanase (GH10) in complex with inhibitor (XIP) -

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Basic information

Entry
Database: PDB / ID: 1ta3
TitleCrystal Structure of xylanase (GH10) in complex with inhibitor (XIP)
Components
  • Endo-1,4-beta-xylanase
  • xylanase inhibitor protein I
KeywordsHYDROLASE INHIBITOR/HYDROLASE / BETA ALPHA BARREL (XIP-I) / BETA ALPHA BARREL (XYLANASE) / HYDROLASE INHIBITOR-HYDROLASE COMPLEX
Function / homology
Function and homology information


enzyme inhibitor activity / chitinase activity / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / defense response to fungus / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitinase Cts1-like / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycosidases / Glycoside hydrolase superfamily ...Chitinase Cts1-like / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase C / Xylanase inhibitor protein 1
Similarity search - Component
Biological speciesEmericella nidulans (mold)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPayan, F. / Leone, P. / Furniss, C. / Tahir, T. / Durand, A. / Porciero, S. / Manzanares, P. / Williamson, G. / Gilbert, H.J. / Juge, N. / Roussel, A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Dual Nature of the Wheat Xylanase Protein Inhibitor XIP-I: STRUCTURAL BASIS FOR THE INHIBITION OF FAMILY 10 AND FAMILY 11 XYLANASES.
Authors: Payan, F. / Leone, P. / Porciero, S. / Furniss, C. / Tahir, T. / Williamson, G. / Durand, A. / Manzanares, P. / Gilbert, H.J. / Juge, N. / Roussel, A.
History
DepositionMay 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 999SEQUENCE THE AUTHORS BELIEVE THAT THESE RESIDUES ARE CORRECT AND GENEBANK IS INCORRECT AT THESE ...SEQUENCE THE AUTHORS BELIEVE THAT THESE RESIDUES ARE CORRECT AND GENEBANK IS INCORRECT AT THESE POSITIONS (SEE PDB ENTRY 1OM0).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,26211
Polymers63,3852
Non-polymers8779
Water14,142785
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.730, 75.872, 159.654
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 xylanase inhibitor protein I / XIP-1


Mass: 30323.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L5C6
#2: Protein Endo-1,4-beta-xylanase / GH10 / 34 kDa xylanase / 1 / 4-beta-D-xylan xylanohydrolase / X34


Mass: 33061.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Gene: XLNC / Production host: Emericella nidulans (mold) / References: UniProt: Q00177, endo-1,4-beta-xylanase
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 785 / 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: 2.24 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 8000, 0.1 M Hepes, 20% ethylen glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Jun 28, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 62367 / % possible obs: 96.9 % / Rsym value: 0.061 / Net I/σ(I): 12.2
Reflection shellResolution: 1.7→1.76 Å / % possible obs: 90 % / Redundancy: 2.6 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.17

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.459 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16554 2498 4.1 %RANDOM
Rwork0.1333 ---
all0.134 ---
obs0.13463 59134 97.22 %-
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: 9.885 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4461 0 56 785 5302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214636
X-RAY DIFFRACTIONr_bond_other_d0.0020.023934
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.936295
X-RAY DIFFRACTIONr_angle_other_deg0.83439146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1155573
X-RAY DIFFRACTIONr_chiral_restr0.090.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025246
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02975
X-RAY DIFFRACTIONr_nbd_refined0.2310.2932
X-RAY DIFFRACTIONr_nbd_other0.2490.24666
X-RAY DIFFRACTIONr_nbtor_other0.0840.22547
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2534
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3610.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.249
X-RAY DIFFRACTIONr_mcbond_it0.7271.52842
X-RAY DIFFRACTIONr_mcangle_it1.32424529
X-RAY DIFFRACTIONr_scbond_it2.24731794
X-RAY DIFFRACTIONr_scangle_it3.4414.51766
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.188 199
Rwork0.149 4037

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