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Yorodumi- PDB-2uvg: Structure of a periplasmic oligogalacturonide binding protein fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uvg | ||||||
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Title | Structure of a periplasmic oligogalacturonide binding protein from Yersinia enterocolitica | ||||||
Components | ABC TYPE PERIPLASMIC SUGAR-BINDING PROTEIN | ||||||
Keywords | SUGAR BINDING PROTEIN / YERSINIA ENTEROCOLITICA / PERIPLASMIC BINDING PROTEIN / TOGB / OLIGALACTURONIDE / PECTIN DEGRADATION / SUGAR-BINDING PROTEIN | ||||||
Function / homology | Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta Function and homology information | ||||||
Biological species | YERSINIA ENTEROCOLITICA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Abbott, D.W. / Boraston, A.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Specific Recognition of Saturated and 4,5-Unsaturated Hexuronate Sugars by a Periplasmic Binding Protein Involved in Pectin Catabolism. 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 | 2uvg.cif.gz | 100.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uvg.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 2uvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uvg_validation.pdf.gz | 427.4 KB | Display | wwPDB validaton report |
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Full document | 2uvg_full_validation.pdf.gz | 438.5 KB | Display | |
Data in XML | 2uvg_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 2uvg_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/2uvg ftp://data.pdbj.org/pub/pdb/validation_reports/uv/2uvg | HTTPS FTP |
-Related 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: 46336.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 44.8 % |
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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: 2.2→20 Å / Num. obs: 20810 / % possible obs: 96.2 % / Observed criterion σ(I): 3 / Redundancy: 3.58 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→65.94 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.012 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.257 / 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: 22.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→65.94 Å
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Refine LS restraints |
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