+Open data
-Basic information
Entry | Database: PDB / ID: 5fpx | ||||||
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Title | The structure of KdgF from Yersinia enterocolitica. | ||||||
Components |
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Keywords | HYDROLASE / KDGF / PECTIN / ALGINATE / URONATE SUGAR METABOLISM / CUPIN | ||||||
Function / homology | Function and homology information Pectin degradation protein KdgF / : / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | YERSINIA ENTEROCOLITICA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Hobbs, J.K. / Lee, S.M. / Robb, M. / Hof, F. / Barr, C. / Abe, K.T. / Hehemann, J.H. / McLean, R. / Abbott, D.W. / Boraston, A.B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Kdgf, the Missing Link in the Microbial Metabolism of Uronate Sugars from Pectin and Alginate. Authors: Hobbs, J.K. / Lee, S.M. / Robb, M. / Hof, F. / Barr, C. / Abe, K.T. / Hehemann, J. / Mclean, R. / Abbott, D.W. / Boraston, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fpx.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fpx.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fpx_validation.pdf.gz | 451.4 KB | Display | wwPDB validaton report |
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Full document | 5fpx_full_validation.pdf.gz | 452.9 KB | Display | |
Data in XML | 5fpx_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 5fpx_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/5fpx ftp://data.pdbj.org/pub/pdb/validation_reports/fp/5fpx | HTTPS FTP |
-Related structure data
Related structure data | 5fpzC 5fq0C 2pfwS 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: 12826.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Strain: SUBSP. ENTEROCOLITICA 8081 / Plasmid: PET28A-YEKDGF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1JMF7 #2: Protein/peptide | Mass: 939.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Strain: SUBSP. ENTEROCOLITICA 8081 / Plasmid: PET28A-YEKDGF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.02 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 39140 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.6 / % possible all: 78.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PFW Resolution: 1.5→55.33 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.596 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.368 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→55.33 Å
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Refine LS restraints |
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