[English] 日本語
Yorodumi- PDB-5uil: X-ray structure of the FdtF N-formyltransferase from Salmonella e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uil | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of the FdtF N-formyltransferase from Salmonella enterica O60 in complex with TDP-Fuc3N and tetrahydrofolate | ||||||
Components | Formyltransferase | ||||||
Keywords | TRANSFERASE / ankyrin repeat / 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
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5uil.cif.gz | 187.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5uil.ent.gz | 145.6 KB | Display | PDB format |
PDBx/mmJSON format | 5uil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uil_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5uil_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 5uil_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 5uil_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/5uil ftp://data.pdbj.org/pub/pdb/validation_reports/ui/5uil | HTTPS FTP |
-Related structure data
Related structure data | 5uijSC 5uikC 5uimC 5uinC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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): Rosetta2(DE3) / References: UniProt: U3GK13 #2: Chemical | #3: Chemical | ChemComp-T3F / ( #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.36 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 100 mM CHES 200 mM NMe4Cl 12-16% PEG 5000 10 mM TDP-Fuc3N 10 mM N-10-formyltetrahydrofolate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 46550 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4899 / Rsym value: 0.321 / % possible all: 80.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5uij Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.876 / SU B: 8.909 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.246 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.089 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.2→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|