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Yorodumi- PDB-5uik: X-ray structure of the FdtF formyltransferase from salmonella ent... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uik | ||||||
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Title | X-ray structure of the FdtF formyltransferase from salmonella enteric O60 in complex with TDP-Fuc3N and folinic acid | ||||||
Components | Formyltransferase | ||||||
Keywords | TRANSFERASE / ankyrin / lipopolysaccharide / O-antigen | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Salmonella choleraesuis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Woodford, C.R. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Struct. Biol. / Year: 2017 Title: Molecular architecture of an N-formyltransferase from Salmonella enterica O60. Authors: Woodford, C.R. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uik.cif.gz | 187 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uik.ent.gz | 145.2 KB | Display | PDB format |
PDBx/mmJSON format | 5uik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uik_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 5uik_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 5uik_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 5uik_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/5uik ftp://data.pdbj.org/pub/pdb/validation_reports/ui/5uik | HTTPS FTP |
-Related structure data
Related structure data | 5uijSC 5uilC 5uimC 5uinC 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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Unit cell |
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-Components
#1: Protein | Mass: 46415.215 Da / Num. of mol.: 2 / Mutation: E395A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella choleraesuis (bacteria) / Gene: fdtF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosertta2(De3) / References: UniProt: U3GK13 #2: Chemical | ChemComp-T3F / ( #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 100 mM CHES 12-16% PEG 5000 200 mM NMe4Cl 10 mM folinic acid 10 mM TDP-Fuc3N |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: May 18, 2016 / Details: montel |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 46716 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2 / Num. unique obs: 5541 / Rsym value: 0.364 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UIJ Resolution: 2.2→48.09 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.885 / SU B: 8.743 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.242 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.844 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→48.09 Å
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Refine LS restraints |
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