+Open data
-Basic information
Entry | Database: PDB / ID: 3ri8 | ||||||
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Title | Xylanase C from Aspergillus kawachii D37N mutant | ||||||
Components | Endo-1,4-beta-xylanase 3Xylanase | ||||||
Keywords | HYDROLASE / beta-jellyroll / Extracellular | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Aspergillus kawachii (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Fushinobu, S. / Uno, T. / Kitaoka, M. / Hayashi, K. / Matsuzawa, H. / Wakagi, T. | ||||||
Citation | Journal: J.APPL.GLYOSCI. / Year: 2011 Title: Mutational analysis of fungal family 11 xylanases on pH optimum determination Authors: Fushinobu, S. / Uno, T. / Kitaoka, M. / Hayashi, K. / Matsuzawa, H. / Wakagi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ri8.cif.gz | 49.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ri8.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ri8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/3ri8 ftp://data.pdbj.org/pub/pdb/validation_reports/ri/3ri8 | HTTPS FTP |
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-Related structure data
Related structure data | 3ri9C 1bk1S 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: 20024.199 Da / Num. of mol.: 1 / Mutation: D37N Source method: isolated from a genetically manipulated source Details: Co-expression with pT-groE / Source: (gene. exp.) Aspergillus kawachii (mold) / Strain: IFO 4308 / Gene: xynC / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33557, endo-1,4-beta-xylanase |
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#2: Water | ChemComp-HOH / |
Sequence details | SWISSPROT CONTAINS ERRORS AT THESE POSITIONS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5M sodium sulfate, 0.1M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 3, 1998 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→80 Å / Num. all: 15679 / Num. obs: 14918 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.041 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 2.8 / Num. unique all: 1304 / Rsym value: 0.359 / % possible all: 86.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1BK1 Resolution: 2→34.7 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.183 / SU ML: 0.111 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.153 / 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: 35.067 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→34.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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