+Open data
-Basic information
Entry | Database: PDB / ID: 8fuw | ||||||
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Title | KpsC D160N Kdo adduct | ||||||
Components | Capsule polysaccharide export protein KpsC | ||||||
Keywords | TRANSFERASE / glycosyltransferase / retaining | ||||||
Function / homology | Capsule polysaccharide biosynthesis / Capsule polysaccharide biosynthesis protein / polysaccharide transport / polysaccharide biosynthetic process / CYTIDINE-5'-MONOPHOSPHATE / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / Capsule polysaccharide export protein KpsC Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kimber, M.S. / Doyle, L. / Whitfield, C. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Mechanism and linkage specificities of the dual retaining beta-Kdo glycosyltransferase modules of KpsC from bacterial capsule biosynthesis. Authors: Doyle, L. / Ovchinnikova, O.G. / Huang, B.S. / Forrester, T.J.B. / Lowary, T.L. / Kimber, M.S. / Whitfield, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fuw.cif.gz | 239.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fuw.ent.gz | 162.4 KB | Display | PDB format |
PDBx/mmJSON format | 8fuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fuw_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8fuw_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8fuw_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 8fuw_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/8fuw ftp://data.pdbj.org/pub/pdb/validation_reports/fu/8fuw | HTTPS FTP |
-Related structure data
Related structure data | 8fuxC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36489.590 Da / Num. of mol.: 1 / Mutation: D160N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kpsC / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2Z2W8 | ||||||
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#2: Chemical | ChemComp-C5P / | ||||||
#3: Sugar | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M lithium sulfate, 29 % (v/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5 and 2 mM strontium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98011 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.4 Å / Num. obs: 27085 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 42.94 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.084 / Net I/σ(I): 12.74 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 1.09 / Num. unique obs: 2008 / CC1/2: 0.542 / Rrim(I) all: 2.66 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.4 Å / SU ML: 0.2316 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5086 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.4 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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