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Open data
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Basic information
Entry | Database: PDB / ID: 3ri9 | ||||||
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Title | Xylanase C from Aspergillus kawachii F131W mutant | ||||||
![]() | Endo-1,4-beta-xylanase 3![]() | ||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fushinobu, S. / Uno, T. / Kitaoka, M. / Hayashi, K. / Matsuzawa, H. / Wakagi, T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.4 KB | Display | ![]() |
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PDB format | ![]() | 34.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ri8C ![]() 1bk1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 20064.219 Da / Num. of mol.: 1 / Mutation: F131W Source method: isolated from a genetically manipulated source Details: Co-expression with pT-groE / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
Sequence details | SWISSPROT CONTAINS ERRORS AT THESE POSITIONS |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.99 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 26, 2001 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→32.28 Å / Num. all: 15718 / Num. obs: 15716 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.043 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.11 Å / Mean I/σ(I) obs: 2.8 / Num. unique all: 2229 / Rsym value: 0.26 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1BK1 Resolution: 2→29.98 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.466 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R Free: 0.135 / 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: 38.902 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.98 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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