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- PDB-3hd8: Crystal structure of the Triticum aestivum xylanase inhibitor-IIA... -

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Basic information

Entry
Database: PDB / ID: 3hd8
TitleCrystal structure of the Triticum aestivum xylanase inhibitor-IIA in complex with bacillus subtilis xylanase
Components
  • Endo-1,4-beta-xylanase A
  • Xylanase inhibitor
KeywordsHYDROLASE INHIBITOR/HYDROLASE / TWO BETA-BARREL DOMAIN / BETA-JELLY ROLL / HYDROLASE INHIBITOR-HYDROLASE COMPLEX / PROTEIN-PROTEIN COMPLEX / Xylan degradation / Glycosidase / Hydrolase
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 speciesTriticum aestivum (bread wheat)
Bacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsSansen, S. / Pollet, A. / Raedschelders, G. / Gebruers, K. / Rabijns, A. / Courtin, C.M.
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
DepositionMay 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xylanase inhibitor
B: Endo-1,4-beta-xylanase A
C: Xylanase inhibitor
D: Endo-1,4-beta-xylanase A


Theoretical massNumber of molelcules
Total (without water)121,4224
Polymers121,4224
Non-polymers00
Water75742
1
A: Xylanase inhibitor
B: Endo-1,4-beta-xylanase A


Theoretical massNumber of molelcules
Total (without water)60,7112
Polymers60,7112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Xylanase inhibitor
D: Endo-1,4-beta-xylanase A


Theoretical massNumber of molelcules
Total (without water)60,7112
Polymers60,7112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.351, 60.300, 134.187
Angle α, β, γ (deg.)90.00, 101.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1110A1 - 389
2110C1 - 389
1120B1 - 185
2120D1 - 185

NCS ensembles :
ID
1
2

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Components

#1: Protein Xylanase inhibitor / Xylanase Inhibitor IIA


Mass: 40302.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Gene: XYNA / Plasmid: pPICZaC / Production host: Pichia pastoris (fungus) / References: UniProt: Q53IQ4
#2: Protein Endo-1,4-beta-xylanase A / Xylanase A / 1 / 4-beta-D-xylan xylanohydrolase A


Mass: 20409.004 Da / Num. of mol.: 2
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


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsBASED ON THE PAPER (PMID: 16084833) DESCRIBING THE TAXI-IIA SEQUENCE (CHAINS A AND C) THE CORRECT ...BASED ON THE PAPER (PMID: 16084833) DESCRIBING THE TAXI-IIA SEQUENCE (CHAINS A AND C) THE CORRECT SEQUENCE SHOULD BE GLU1, PRO163 AND LEU314. FOR THE XYLANASE (CHAINS B AND D) RESIDUE 147 SHOULD BE SERINE.

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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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 18% (w/v) polyethylene glycol 4000, 0.18M ammonium sulfate, 0.1M sodium acetate buffer , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.811 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 4, 2005
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. all: 48031 / Num. obs: 45604 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.076 / Net I/σ(I): 7.7
Reflection shellResolution: 2.38→2.44 Å / Mean I/σ(I) obs: 3.8 / Num. unique all: 955 / Rsym value: 0.341 / % possible all: 97.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1T6E for chains A and C; 1C5H for the chains B and D

1t6e

1c5h


Resolution: 2.39→38.52 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.88 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.539 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.444 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27459 2427 5.1 %RANDOM
Rwork0.22344 ---
obs0.22601 44570 98.77 %-
all-45713 --
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 max: 91.7 Å2 / Biso mean: 38.726 Å2 / Biso min: 15.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å21.15 Å2
2--0.58 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.39→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8240 0 0 42 8282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0218474
X-RAY DIFFRACTIONr_bond_other_d0.0040.027450
X-RAY DIFFRACTIONr_angle_refined_deg2.2371.94211588
X-RAY DIFFRACTIONr_angle_other_deg1.222317328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.19151096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1280.21280
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029586
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021736
X-RAY DIFFRACTIONr_nbd_refined0.2420.21672
X-RAY DIFFRACTIONr_nbd_other0.2650.28523
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.10.25130
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3470.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3510.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0680.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0631.55468
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.95128768
X-RAY DIFFRACTIONr_scbond_it2.63133006
X-RAY DIFFRACTIONr_scangle_it4.314.52820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A5199TIGHT POSITIONAL0.070.05
1A5199TIGHT THERMAL0.40.5
2B2636TIGHT POSITIONAL0.080.05
2B2636TIGHT THERMAL0.370.5
LS refinement shellResolution: 2.387→2.448 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.403 153
Rwork0.364 2935
all-3088

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