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- PDB-1uqy: Xylanase Xyn10B mutant (E262S) from Cellvibrio mixtus in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1uqy | |||||||||
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Title | Xylanase Xyn10B mutant (E262S) from Cellvibrio mixtus in complex with xylopentaose | |||||||||
![]() | ENDOXYLANASE | |||||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Pell, G. / Taylor, E.J. / Gloster, T.M. / Turkenburg, J.P. / Fontes, C.M.G.A. / Ferreira, L.M.A. / Davies, G.J. / Gilbert, H.J. | |||||||||
![]() | ![]() Title: The Mechanisms by which Family 10 Glycoside Hydrolases Bind Decorated Substrates Authors: Pell, G. / Taylor, E.J. / Gloster, T.M. / Turkenburg, J.P. / Fontes, C.M.G.A. / Ferreira, L.M.A. / Nagy, T. / Clark, S. / Davies, G.J. / Gilbert, H.J. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101 KB | Display | ![]() |
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PDB format | ![]() | 74.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1uqzC ![]() 1ur1C ![]() 1ur2C ![]() 1clxS C: citing same article ( S: Starting model for refinement |
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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: 42949.910 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 11-379 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ENGINEERED MUTATION GLU 262 SER IN COORDS / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose![]() Source method: isolated from a genetically manipulated source | ||
#3: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose![]() Source method: isolated from a genetically manipulated source | ||
#4: Chemical | ChemComp-MG / | ||
#5: Water | ChemComp-HOH / ![]() | ||
Compound details | ENGINEEREDSequence details | THE SEQUENCE ON THE DATABASE IS INCORRECT AND WILL BE CHANGED BY THE AUTHORS. THESE DISCREPANCIES ...THE SEQUENCE ON THE DATABASE IS INCORRECT AND WILL BE CHANGED BY THE AUTHORS. THESE DISCREPANC | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 36.6 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | pH: 8 / Details: 0.2M MGCL2 0.1M TRIS HCL PH8, 30% PEG 4K, pH 8.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2003 / Details: OSMICS |
Radiation | Monochromator: MULTI-LAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.72→20 Å / Num. obs: 34539 / % possible obs: 99.6 % / Redundancy: 6.02 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 46 |
Reflection shell | Resolution: 1.72→1.78 Å / Redundancy: 5.49 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 10.35 / % possible all: 98.7 |
Reflection | *PLUS Highest resolution: 1.72 Å / Lowest resolution: 20 Å / Redundancy: 6.02 % / Rmerge(I) obs: 0.038 |
Reflection shell | *PLUS % possible obs: 98.7 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 10.35 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1CLX Resolution: 1.72→56.8 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.774 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY HAS SOME ATOMS WHICH HAVE BEEN REFINED WITH AN OCCUPANCY OF 0.00
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→56.8 Å
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Refine LS restraints |
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