+Open data
-Basic information
Entry | Database: PDB / ID: 3g7m | ||||||
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Title | Structure of the thaumatin-like xylanase inhibitor TLXI | ||||||
Components | Xylanase inhibitor TL-XI | ||||||
Keywords | HYDROLASE INHIBITOR / beta-sheets / Xylan degradation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Triticum aestivum (bread wheat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | ||||||
Authors | Vandermarliere, E. / Courtin, C.M. / Lammens, W. / Schoepe, J. / Strelkov, S.V. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g7m.cif.gz | 41.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g7m.ent.gz | 28.1 KB | Display | PDB format |
PDBx/mmJSON format | 3g7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/3g7m ftp://data.pdbj.org/pub/pdb/validation_reports/g7/3g7m | HTTPS FTP |
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-Related structure data
Related structure data | 1kwn S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.17 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9762 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 4, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KWN 1kwn 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.313 Å2
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Refinement step | Cycle: LAST / Resolution: 2.91→19.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.906→2.98 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -42.2264 Å / Origin y: 12.5156 Å / Origin z: -12.8718 Å
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