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- PDB-3f0q: Staphylococcus aureus dihydrofolate reductase complexed with NADP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f0q | ||||||
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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 | ||||||
![]() | Trimethoprim-sensitive dihydrofolate reductase | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / Chem-52V / Chem-NDP / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Anderson, A.C. / Frey, K.M. / Liu, J. / Lombardo, M.N. | ||||||
![]() | ![]() Title: Predicting resistance mutations using protein design algorithms. Authors: Frey, K.M. / Georgiev, I. / Donald, B.R. / Anderson, A.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.7 KB | Display | ![]() |
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PDB format | ![]() | 35.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 982.3 KB | Display | ![]() |
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Full document | ![]() | 985.4 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18015.557 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-52V / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.96 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: LAST / Resolution: 2.08→25.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.29 Å / Total num. of bins used: 20
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