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Yorodumi- PDB-1t6g: Crystal structure of the Triticum aestivum xylanase inhibitor-I i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t6g | ||||||
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Title | Crystal structure of the Triticum aestivum xylanase inhibitor-I in complex with aspergillus niger xylanase-I | ||||||
Components |
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Keywords | HYDROLASE INHIBITOR / protein-protein complex / two beta-barrel domain structure / beta-jelly roll structure | ||||||
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 / extracellular region Similarity search - Function | ||||||
Biological species | Triticum aestivum (bread wheat) Aspergillus niger (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sansen, S. / De Ranter, C.J. / Gebruers, K. / Brijs, K. / Courtin, C.M. / Delcour, J.A. / Rabijns, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I Authors: Sansen, S. / De Ranter, C.J. / Gebruers, K. / Brijs, K. / Courtin, C.M. / Delcour, J.A. / Rabijns, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t6g.cif.gz | 234.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t6g.ent.gz | 186.4 KB | Display | PDB format |
PDBx/mmJSON format | 1t6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/1t6g ftp://data.pdbj.org/pub/pdb/validation_reports/t6/1t6g | HTTPS FTP |
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-Related structure data
Related structure data | 1t6eSC 1ukrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 38862.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: purified from wheat flour / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8H0K8, endo-1,4-beta-xylanase #2: Protein | Mass: 19893.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger (mold) / References: UniProt: P55329, endo-1,4-beta-xylanase #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 51.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.25 M magnesium acetate 0.1 M sodium cacodylate buffer, 17% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 4, 2002 |
Radiation | Monochromator: Sagitally focusing Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29.74 Å / Num. all: 104587 / Num. obs: 93187 / % possible obs: 89.1 % / Observed criterion σ(F): 1.41 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.8→1.9 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T6E, 1UKR Resolution: 1.8→29.74 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.02 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.111 / 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: 14.576 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→29.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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