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- PDB-2y64: Xylopentaose binding mutated (X-2 L110F) CBM4-2 Carbohydrate Bind... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y64 | |||||||||
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Title | Xylopentaose binding mutated (X-2 L110F) CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase | |||||||||
![]() | XYLANASE | |||||||||
![]() | HYDROLASE | |||||||||
Function / homology | ![]() hydrolase activity, acting on glycosyl bonds / xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | von Schantz, L. / Hakansson, M. / Logan, D.T. / Walse, B. / Osterlin, J. / Nordberg-Karlsson, E. / Ohlin, M. | |||||||||
![]() | ![]() Title: Structural basis for carbohydrate-binding specificity--a comparative assessment of two engineered carbohydrate-binding modules. Authors: von Schantz, L. / Hakansson, M. / Logan, D.T. / Walse, B. / Osterlin, J. / Nordberg-Karlsson, E. / Ohlin, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.7 KB | Display | ![]() |
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PDB format | ![]() | 71.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2y6gC ![]() 2y6hSC ![]() 2y6jC ![]() 2y6kC ![]() 2y6lC 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: 17939.734 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 1-165 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q6V8M0, UniProt: Q7WTN6*PLUS, endo-1,4-beta-xylanase | ||||||||
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose- ...beta-D-xylopyranose-(1-4)-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 | ||||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, TYR 68 TO PHE ENGINEERED RESIDUE IN CHAIN A, ASP 69 TO ASN ...ENGINEERED | Nonpolymer details | D-XYLOSE (XYP): XYLOPENTAO | Sequence details | THIS CONSTRUCT STARTS WITH MET (POSITION 1) AS AN INITIATING | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 0.1 M MIB BUFFER PH 6.0, 25 % W/V PEG 1500. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: Mar 10, 2010 / Details: MIRRORS |
Radiation | Monochromator: GERMANIUM CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 30301 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.4→1.44 Å / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.7 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y6H Resolution: 1.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: SWAT | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Refine LS restraints |
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