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Yorodumi- PDB-2vrq: STRUCTURE OF AN INACTIVE MUTANT OF ARABINOFURANOSIDASE FROM THERM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vrq | |||||||||
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Title | STRUCTURE OF AN INACTIVE MUTANT OF ARABINOFURANOSIDASE FROM THERMOBACILLUS XYLANILYTICUS IN COMPLEX WITH A PENTASACCHARIDE | |||||||||
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 / polysaccharide catabolic process Similarity search - Function | |||||||||
Biological species | THERMOBACILLUS XYLANILYTICUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" 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. THE SHEETS PRESENTED AS "BB" 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. THE SHEETS PRESENTED AS "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 | 2vrq.cif.gz | 322.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vrq.ent.gz | 265.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vrq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vrq_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2vrq_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2vrq_validation.xml.gz | 64.2 KB | Display | |
Data in CIF | 2vrq_validation.cif.gz | 95.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/2vrq ftp://data.pdbj.org/pub/pdb/validation_reports/vr/2vrq | HTTPS FTP |
-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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 56183.324 Da / Num. of mol.: 3 / Mutation: YES 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: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-L-arabinofuranose-(1-3)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose | Source method: isolated from a genetically manipulated source #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 176 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 176 TO GLN ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.25 % / 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: 1.078 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 |
Reflection | Resolution: 2→78.33 Å / Num. obs: 184568 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.6 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→78.4 Å / SU ML: 0.22 / σ(F): 1.48 / Phase error: 16.6 / 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: 57.04 Å2 / ksol: 0.39 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→78.4 Å
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Refine LS restraints |
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LS refinement shell |
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