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Yorodumi- PDB-2xvk: crystal structure of alpha-xylosidase (GH31) from Cellvibrio japo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xvk | ||||||
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Title | crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus in complex with 5-fluoro-alpha-D-xylopyranosyl fluoride | ||||||
Components | ALPHA-XYLOSIDASE, PUTATIVE, XYL31A | ||||||
Keywords | HYDROLASE / GLYCOSYL HYDROLASE FAMILY 31 / (BETA/ALPHA) 8 BARREL | ||||||
Function / homology | Function and homology information Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | CELLVIBRIO JAPONICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å | ||||||
Authors | Larsbrink, J. / Izumi, A. / Ibatullin, F. / Nakhai, A. / Gilbert, H.J. / Davies, G.J. / Brumer, H. | ||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: Structural and Enzymatic Characterisation of a Glycoside Hydrolase Family 31 Alpha-Xylosidase from Cellvibrio Japonicus Involved in Xyloglucan Saccharification. Authors: Larsbrink, J. / Izumi, A. / Ibatullin, F. / Nakhai, A. / Gilbert, H.J. / Davies, G.J. / Brumer, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xvk.cif.gz | 397.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xvk.ent.gz | 325.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xvk_validation.pdf.gz | 454.4 KB | Display | wwPDB validaton report |
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Full document | 2xvk_full_validation.pdf.gz | 465.3 KB | Display | |
Data in XML | 2xvk_validation.xml.gz | 34.3 KB | Display | |
Data in CIF | 2xvk_validation.cif.gz | 47.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/2xvk ftp://data.pdbj.org/pub/pdb/validation_reports/xv/2xvk | HTTPS FTP |
-Related structure data
Related structure data | 2xvgC 2xvlC 2g3mS C: citing same article (ref.) S: Starting model for refinement |
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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: 115203.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE OD ATOM OF D582 LINKS TO THE C1 ATOM OF FFX. / Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B3PBD9, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds | ||||||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NI / | #4: Sugar | ChemComp-FFX / ( | #5: Water | ChemComp-HOH / | Nonpolymer details | 5-FLUORO-ALPHA-D-XYLOPYRANOSYL FLUORIDE (FFX): THE FLUORIDE ATOM AT C1 OF THIS LIGAND WAS REMOVED ...5-FLUORO-ALPHA-D-XYLOPYRANO | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.81 % / Description: NONE |
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Crystal grow | pH: 7 Details: 25 % PEG MONOMETHYL ETHER 550 (PEG MME 550), 0.1 M BIS-TRIS (PH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 57181 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 8 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2G3M Resolution: 2.503→49.985 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 25.51 / Stereochemistry target values: ML Details: DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY AND HAVE ZERO OCCUPANCIES.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.99 Å2 / ksol: 0.312 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.503→49.985 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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