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- PDB-1us2: Xylanase10C (mutant E385A) from Cellvibrio japonicus in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1us2 | |||||||||
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Title | Xylanase10C (mutant E385A) from Cellvibrio japonicus in complex with xylopentaose | |||||||||
![]() | ENDO-BETA-1,4-XYLANASE | |||||||||
![]() | HYDROLASE / CARBOHYDRATE BINDING MODULE / XYLAN DEGRADATION | |||||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cell outer membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pell, G. / Szabo, L. / Charnock, S.J. / Xie, H. / Gloster, T.M. / Davies, G.J. / Gilbert, H.J. | |||||||||
![]() | ![]() Title: Structural and Biochemical Analysis of Cellvibrio Japonicus Xylanase 10C: How Variation in Substrate-Binding Cleft Influences the Catalytic Profile of Family Gh-10 Xylanases Authors: Pell, G. / Szabo, L. / Charnock, S.J. / Xie, H. / Gloster, T.M. / Davies, G.J. / Gilbert, H.J. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 | ![]() | 137 KB | Display | ![]() |
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PDB format | ![]() | 103.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 872.8 KB | Display | ![]() |
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Full document | ![]() | 879.9 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 46.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1us3C ![]() 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: 58152.391 Da / Num. of mol.: 1 Fragment: CARBOHYDRATE BINDING MODULE AND CATALYTIC MODULE, RESIDUES (86-606) Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | NUMBERING IS CONSISTENT WITH THE SWISSPROT ENTRY FOR THE GENE. 3 MISTAKES WERE DISCOVERED IN ...NUMBERING IS CONSISTENT | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.9 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 30 MG/ML PROTEIN 0.2 M SODIUM IODIDE, 20% PEG 3350, 20 MM (1 UL) XYLOPENTAOSE, pH 7.00 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2001 / Details: VERTICALLY FOCUSSING RH COATED SI MIRROR |
Radiation | Monochromator: TRIANGULAR SINGLE CRYSTAL SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 53227 / % possible obs: 98 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.8 / % possible all: 98 |
Reflection | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 20 Å / % possible obs: 98 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 98 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CLX Resolution: 1.85→84.52 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 2.556 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: ATOMS THAT COULD NOT BE PLACED RELIABLY IN ELECTRON DENSITY HAVE BEEN SET TO ZERO OCCUPANCY
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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: 14.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→84.52 Å
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Refine LS restraints |
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