[English] 日本語
Yorodumi- PDB-3f0q: Staphylococcus aureus dihydrofolate reductase complexed with NADP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f0q | ||||||
---|---|---|---|---|---|---|---|
Title | Staphylococcus aureus dihydrofolate reductase complexed with NADPH and 2,4-Diamino-5-[3-(3-methoxy-5-(2,6-dimethylphenyl)phenyl)but-1-ynyl]-6-methylpyrimidine | ||||||
Components | Trimethoprim-sensitive dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / Chem-52V / Chem-NDP / : Function and homology information | ||||||
Biological species | Staphylococcus aureus RF122 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.08 Å | ||||||
Authors | Anderson, A.C. / Frey, K.M. / Liu, J. / Lombardo, M.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Predicting resistance mutations using protein design algorithms. Authors: Frey, K.M. / Georgiev, I. / Donald, B.R. / Anderson, A.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3f0q.cif.gz | 50.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3f0q.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 3f0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f0q_validation.pdf.gz | 982.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3f0q_full_validation.pdf.gz | 985.4 KB | Display | |
Data in XML | 3f0q_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 3f0q_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/3f0q ftp://data.pdbj.org/pub/pdb/validation_reports/f0/3f0q | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18015.557 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus RF122 (bacteria) / Gene: dfrB / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YY41, dihydrofolate reductase |
---|---|
#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-52V / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.96 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15 % PEG 10000, 150 mM Sodium acetate, 100 mM MES pH 6.5, 5 % Butyrlactone, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77.2 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→25.92 Å / Num. all: 10908 / Num. obs: 10908 / % possible obs: 87.9 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.08→2.29 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 2.7 / Num. unique all: 782 / Rsym value: 0.143 / % possible all: 95.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: Sa F98Y DHFR bound to Folate and NADPH (Dale et al., J.Mol.Biol. 1997, structure not deposited in the PDB) Resolution: 2.08→25.92 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.57 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.185 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 191.93 Å2 / Biso mean: 20.644 Å2 / Biso min: 6.56 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→25.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.08→2.29 Å / Total num. of bins used: 20
|