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Yorodumi- PDB-1te1: Crystal structure of family 11 xylanase in complex with inhibitor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1te1 | ||||||
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Title | Crystal structure of family 11 xylanase in complex with inhibitor (XIP-I) | ||||||
Components |
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Keywords | HYDROLASE INHIBITOR/HYDROLASE / BETA/ALPHA BARREL (XIP-I) and BETA JELLY ROLL (GH11) / HYDROLASE INHIBITOR-HYDROLASE COMPLEX | ||||||
Function / homology | Function and homology information chitinase activity / enzyme inhibitor 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 | ||||||
Biological species | Penicillium funiculosum (fungus) Triticum aestivum (bread wheat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Payan, F. / Leone, P. / Furniss, C. / Tahir, T. / Durand, A. / Porciero, S. / Manzanares, P. / Williamson, G. / Gilbert, H.J. / Juge, N. / Roussel, A. | ||||||
Citation | Journal: 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 |
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Remark 999 | SEQUENCE 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). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1te1.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1te1.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 1te1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/1te1 ftp://data.pdbj.org/pub/pdb/validation_reports/te/1te1 | HTTPS FTP |
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-Related structure data
Related structure data | 1ta3C 1omoS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30323.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L5C6 | ||||
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#2: Protein | Mass: 20633.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium funiculosum (fungus) / Gene: xynC / Production host: Penicillium funiculosum (fungus) / References: UniProt: Q9HFH0, endo-1,4-beta-xylanase | ||||
#3: Sugar | #4: Chemical | ChemComp-EDO / #5: 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: 2.7 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, ammonium sulfate, 1,2,3-heptanetriol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9785 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 12, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 19734 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 60.5 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.068 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2834 / Rsym value: 0.387 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UKR, PDB ENTRY 1OMO Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.903 / SU B: 11.999 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.635 / ESU R Free: 0.32 / 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: 26.836 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.633 Å / Total num. of bins used: 10 /
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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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