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Yorodumi- PDB-2uvf: Structure of Yersinia enterocolitica Family 28 Exopolygalacturona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uvf | |||||||||
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Title | Structure of Yersinia enterocolitica Family 28 Exopolygalacturonase in Complex with Digalaturonic Acid | |||||||||
Components | EXOPOLYGALACTURONASE | |||||||||
Keywords | HYDROLASE / GH28 / PECTIN / CELL WALL / PERIPLASM / YERSINIA ENTEROCOLITICA / BETA-HELIX / GLYCOSIDASE / EXO-ACTIVITY | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | YERSINIA ENTEROCOLITICA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Abbott, D.W. / Boraston, A.B. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The Structural Basis for Exopolygalacturonase Activity in a Family 28 Glycoside Hydrolase. Authors: Abbott, D.W. / Boraston, A.B. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uvf.cif.gz | 246.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uvf.ent.gz | 196.4 KB | Display | PDB format |
PDBx/mmJSON format | 2uvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/2uvf ftp://data.pdbj.org/pub/pdb/validation_reports/uv/2uvf | HTTPS FTP |
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-Related structure data
Related structure data | 2uveSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 66731.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O68975*PLUS #2: Polysaccharide | alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 5 types, 521 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-NI / #5: Chemical | ChemComp-ACT / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE AUTHORS REPORT THAT THIS IS MANUALLY SEQUENCED ENTRY FROM AN UNKNOWN STRAIN OF Y. ...THE AUTHORS REPORT THAT THIS IS MANUALLY SEQUENCED ENTRY FROM AN UNKNOWN STRAIN OF Y. ENTEROCOLI |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.59 % |
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.54 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→19.72 Å / Num. obs: 75070 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.11 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2UVE Resolution: 2.1→19.72 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.619 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.72 Å
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