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Yorodumi- PDB-2w9g: Wild-type Staphylococcus aureus DHFR in complex with NADPH and tr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w9g | ||||||
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Title | Wild-type Staphylococcus aureus DHFR in complex with NADPH and trimethoprim | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / ONE-CARBON METABOLISM | ||||||
Function / homology | Function and homology information dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Soutter, H.H. / Miller, J.R. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: Structural Comparison of Chromosomal and Exogenous Dihydrofolate Reductase from Staphylococcus Aureus in Complex with the Potent Inhibitor Trimethoprim. Authors: Heaslet, H. / Harris, M. / Fahnoe, K. / Sarver, R. / Putz, H. / Chang, J. / Subramanian, C. / Barreiro, G. / Miller, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w9g.cif.gz | 50.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w9g.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 2w9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/2w9g ftp://data.pdbj.org/pub/pdb/validation_reports/w9/2w9g | HTTPS FTP |
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-Related 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: 18275.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: MU-50 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A017, dihydrofolate reductase |
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#2: Chemical | ChemComp-TOP / |
#3: Chemical | ChemComp-NDP / |
#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: 2.38 Å3/Da / Density % sol: 47.98 % / Description: NONE |
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Crystal grow | pH: 6.4 Details: BUFFER: 30 MM CITRIC ACID / 40 MM BIS-TRIS PROPANE PH6.4, 13.3% PEG3350, 16.7% PEG6000 |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 20, 2007 / Details: SI |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 54341 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 33 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→68.68 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.896 / SU B: 4.401 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.184 / 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 mean: 25.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→68.68 Å
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