+Open data
-Basic information
Entry | Database: PDB / ID: 5fq0 | ||||||
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Title | The structure of KdgF from Halomonas sp. | ||||||
Components |
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Keywords | LYASE / 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 | HALOMONAS SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 | 5fq0.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fq0.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fq0_validation.pdf.gz | 477.6 KB | Display | wwPDB validaton report |
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Full document | 5fq0_full_validation.pdf.gz | 483.7 KB | Display | |
Data in XML | 5fq0_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 5fq0_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/5fq0 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/5fq0 | HTTPS FTP |
-Related structure data
Related structure data | 5fpxSC 5fpzC 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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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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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 12841.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HALOMONAS SP. (bacteria) / Plasmid: PET28A-HAKDGF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A182DWD1*PLUS |
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#2: Protein | Mass: 12818.370 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HALOMONAS SP. (bacteria) / Plasmid: PET28A-HAKDGF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A182DWD2*PLUS |
-Protein/peptide , 1 types, 1 molecules H
#3: Protein/peptide | Mass: 846.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HALOMONAS SP. (bacteria) / Plasmid: PET28A-HAKDGF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) |
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-Non-polymers , 3 types, 290 molecules
#4: Chemical | ChemComp-NI / #5: Chemical | ChemComp-FLC / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.1 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→60 Å / Num. obs: 22373 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FPX Resolution: 2→62.36 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.412 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 30.001 Å2
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Refinement step | Cycle: LAST / Resolution: 2→62.36 Å
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Refine LS restraints |
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