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Yorodumi- PDB-3fqo: Staphylococcus aureus F98Y mutant dihydrofolate reductase complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fqo | ||||||
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Title | Staphylococcus aureus F98Y mutant dihydrofolate reductase complexed with NADPH and 2,4-diamino-5-[3-(2,5-dimethoxyphenyl)prop-1-ynyl]-6-ethylpyrimidine (UCP120B) | ||||||
Components | Trimethoprim-sensitive dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / Chem-N22 / Chem-NDP / : Function and homology information | ||||||
Biological species | Staphylococcus aureus RF122 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.09 Å | ||||||
Authors | Anderson, A.C. / Frey, K.M. / Liu, J. / Lombardo, M.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fqo.cif.gz | 49.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fqo.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 3fqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fqo_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3fqo_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3fqo_validation.xml.gz | 10 KB | Display | |
Data in CIF | 3fqo_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/3fqo ftp://data.pdbj.org/pub/pdb/validation_reports/fq/3fqo | HTTPS FTP |
-Related structure data
Related structure data | 3f0bC 3f0uC 3fq0C 3fqcC 3fqfC 3fqvC 3fqzC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Staphylococcus aureus RF122 (bacteria) / Strain: RF122 / ET3-1 / Gene: dfrB, SAB1281c / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YY41, dihydrofolate reductase |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-N22 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.18 % |
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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: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
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: 2.09→42.33 Å / Num. obs: 11685 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 9.4 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.09→2.18 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.8 / Num. unique all: 838 / Rsym value: 0.406 / % possible all: 100 |
-Processing
Software |
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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: 2.09→42.33 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.232 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.196 / 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: 61.56 Å2 / Biso mean: 30.258 Å2 / Biso min: 5.04 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→42.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.18 Å / Total num. of bins used: 20
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