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- PDB-3fqf: Staphylococcus aureus F98Y mutant dihydrofolate reductase complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fqf | ||||||
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Title | Staphylococcus aureus F98Y mutant dihydrofolate reductase complexed with NADPH and 2,4-diamino-5-[3-(3,4,5-trimethoxyphenyl)pent-1-ynyl]-6-methylpyrimidine (UCP115A) | ||||||
![]() | Trimethoprim-sensitive dihydrofolate reductase | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / Chem-55V / Chem-NDP / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Anderson, A.C. / Frey, K.M. / Liu, J. / Lombardo, M.N. | ||||||
![]() | ![]() Title: Crystal structures of wild-type and mutant methicillin-resistant Staphylococcus aureus dihydrofolate reductase reveal an alternate conformation of NADPH that may be linked to trimethoprim resistance. Authors: Frey, K.M. / Liu, J. / Lombardo, M.N. / Bolstad, D.B. / Wright, D.L. / 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 | ![]() | 52.7 KB | Display | ![]() |
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PDB format | ![]() | 37 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 994.4 KB | Display | ![]() |
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Full document | ![]() | 1000 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f0bC ![]() 3f0uC ![]() 3fq0C ![]() 3fqcC ![]() 3fqoC ![]() 3fqvC ![]() 3fqzC C: citing same article ( |
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Similar 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: 18031.557 Da / Num. of mol.: 1 / Mutation: F98Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-55V / |
#3: Chemical | ChemComp-NDP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG 10000, 150mM Sodium acetate, 100mM 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: Apr 19, 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: 1.77→32.72 Å / Num. obs: 17214 / % possible obs: 89.4 % / Observed criterion σ(I): 3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 1.4 |
Reflection shell | Resolution: 1.77→1.82 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 1.1 / Num. unique all: 1374 / Rsym value: 0.167 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: Sa F98Y DHFR bound to Folate and NADPH (Dale et al., J.Mol.Biol. 1997, structure not deposited in the PDB) Resolution: 1.77→32.72 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.501 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.137 / 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: 150.32 Å2 / Biso mean: 14.909 Å2 / Biso min: 3.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→32.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.82 Å / Total num. of bins used: 20
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