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Yorodumi- PDB-2vrk: Structure of a seleno-methionyl derivative of wild type arabinofu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vrk | ||||||
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Title | Structure of a seleno-methionyl derivative of wild type arabinofuranosidase from Thermobacillus xylanilyticus | ||||||
Components | ALPHA-L-ARABINOFURANOSIDASE | ||||||
Keywords | HYDROLASE / GLYCOSIDASE | ||||||
Function / homology | Function and homology information L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity Similarity search - Function | ||||||
Biological species | THERMOBACILLUS XYLANILYTICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Paes, G. / Skov, L.K. / ODonohue, M.J. / Remond, C. / Kastrup, J.S. / Gajhede, M. / Mirza, O. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: The Structure of the Complex between a Branched Pentasaccharide and Thermobacillus Xylanilyticus Gh-51 Arabinofuranosidase Reveals Xylan-Binding Determinants and Induced Fit. Authors: Paes, G. / Skov, L.K. / O'Donohue, M.J. / Remond, C. / Kastrup, J.S. / Gajhede, M. / Mirza, O. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "BB", "CB" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "BB", "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vrk.cif.gz | 319.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vrk.ent.gz | 272.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vrk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/2vrk ftp://data.pdbj.org/pub/pdb/validation_reports/vr/2vrk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 56934.625 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOBACILLUS XYLANILYTICUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) References: UniProt: O69262, non-reducing end alpha-L-arabinofuranosidase #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67.05 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9789 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→39.47 Å / Num. obs: 188045 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 37.35 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.6 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.2→39.5 Å / SU ML: 0.24 / Phase error: 15.03 / Stereochemistry target values: ML Details: THE FIRST 3 RESIDUES WERE NOT MODELED DUE TO POOR DENSITY.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.19 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→39.5 Å
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Refine LS restraints |
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