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- PDB-3g7m: Structure of the thaumatin-like xylanase inhibitor TLXI -

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Basic information

Entry
Database: PDB / ID: 3g7m
TitleStructure of the thaumatin-like xylanase inhibitor TLXI
ComponentsXylanase inhibitor TL-XI
KeywordsHYDROLASE INHIBITOR / beta-sheets / Xylan degradation
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / xylan catabolic process / defense response
Similarity search - Function
Thaumatin / Thaumatin / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Thaumatin-like xylanase inhibitor
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsVandermarliere, E. / Courtin, C.M. / Lammens, W. / Schoepe, J. / Strelkov, S.V.
CitationJournal: Proteins / Year: 2010
Title: Crystal structure of the noncompetitive xylanase inhibitor TLXI, member of the small thaumatin-like protein family.
Authors: Vandermarliere, E. / Lammens, W. / Schoepe, J. / Rombouts, S. / Fierens, E. / Gebruers, K. / Volckaert, G. / Rabijns, A. / Delcour, J.A. / Strelkov, S.V. / Courtin, C.M.
History
DepositionFeb 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylanase inhibitor TL-XI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6923
Polymers15,5771
Non-polymers1152
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Xylanase inhibitor TL-XI
hetero molecules

A: Xylanase inhibitor TL-XI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3846
Polymers31,1532
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-11
Buried area2390 Å2
ΔGint-21 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.019, 104.019, 30.047
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-161-

HOH

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Components

#1: Protein Xylanase inhibitor TL-XI


Mass: 15576.720 Da / Num. of mol.: 1 / Mutation: H22A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Gene: tlxi / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q0WX48
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium sulfate, 0.1M acetate buffer pH 4.6, 25% PEG 4000, 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: 0.9762 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 4257 / Num. obs: 4255 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Rsym value: 0.081 / Net I/σ(I): 12.4
Reflection shellResolution: 2.9→3.1 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 204 / Rsym value: 0.286 / % possible all: 98.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.2.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KWN

1kwn
PDB Unreleased entry


Resolution: 2.91→19.21 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.813 / SU B: 46.856 / SU ML: 0.384 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.512 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28613 819 19.3 %RANDOM
Rwork0.22822 ---
obs0.23948 3433 99.91 %-
all-4257 --
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: 21.313 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å20 Å2
2---0.09 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.91→19.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 7 27 1120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221126
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9631534
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2475150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80823.24337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7715161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.992156
X-RAY DIFFRACTIONr_chiral_restr0.0890.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021848
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.421.5744
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.76621190
X-RAY DIFFRACTIONr_scbond_it1.1793382
X-RAY DIFFRACTIONr_scangle_it1.9914.5344
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.906→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 57 -
Rwork0.324 245 -
obs--98.69 %
Refinement TLS params.Method: refined / Origin x: -42.2264 Å / Origin y: 12.5156 Å / Origin z: -12.8718 Å
111213212223313233
T0.0741 Å2-0.0287 Å2-0.0277 Å2-0.0356 Å20.0074 Å2--0.081 Å2
L1.8134 °2-1.6486 °2-0.4491 °2-3.3082 °20.4207 °2--2.5322 °2
S-0.0688 Å °-0.0981 Å °-0.0525 Å °0.2217 Å °0.0171 Å °-0.0733 Å °0.1449 Å °0.1262 Å °0.0516 Å °

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