+Open data
-Basic information
Entry | Database: PDB / ID: 3fy9 | ||||||
---|---|---|---|---|---|---|---|
Title | Staph. aureus DHFR F98Y complexed with AR-102 | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / DHFR / AR-102 / NADP / One-carbon metabolism | ||||||
Function / homology | Function and homology information glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Oefner, C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Inhibitory properties and X-ray crystallographic study of the binding of AR-101, AR-102 and iclaprim in ternary complexes with NADPH and dihydrofolate reductase from Staphylococcus aureus Authors: Oefner, C. / Parisi, S. / Schulz, H. / Lociuro, S. / Dale, G.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3fy9.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3fy9.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 3fy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/3fy9 ftp://data.pdbj.org/pub/pdb/validation_reports/fy/3fy9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3fy8SC 3fyvC 3fywC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18160.736 Da / Num. of mol.: 1 / Mutation: F98Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A017, dihydrofolate reductase |
---|---|
#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-XCF / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.83 % |
---|---|
Crystal grow | pH: 5.5 / Details: 25% PEG3350, 200mM NaCl, 100mM bis-Tris, pH5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 23, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. all: 9334 / Num. obs: 8692 / % possible obs: 91.6 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6 / Rmerge(I) obs: 0.181 / Rsym value: 0.181 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FY8 Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.849 / SU B: 12.803 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.225 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.37 Å / Total num. of bins used: 10
|