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Yorodumi- PDB-3fl9: Crystal structure of B. anthracis dihydrofolate reductase (DHFR) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fl9 | ||||||
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Title | Crystal structure of B. anthracis dihydrofolate reductase (DHFR) with trimethoprim | ||||||
Components | dihydrofolate reductase (DHFR) | ||||||
Keywords | OXIDOREDUCTASE / PYRIMIDINE / DIHYDROPHTHALAZINE | ||||||
Function / homology | Function and homology information glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Bourne, C.R. / Barrow, W.W. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2009 Title: Crystal structure of Bacillus anthracis dihydrofolate reductase with the dihydrophthalazine-based trimethoprim derivative RAB1 provides a structural explanation of potency and selectivity. Authors: Bourne, C.R. / Bunce, R.A. / Bourne, P.C. / Berlin, K.D. / Barrow, E.W. / Barrow, W.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fl9.cif.gz | 278 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fl9.ent.gz | 225.3 KB | Display | PDB format |
PDBx/mmJSON format | 3fl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/3fl9 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/3fl9 | HTTPS FTP |
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-Related structure data
Related structure data | 3fl8C 2qk8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19615.453 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS2083, BA_2237, dfrA, DHFR, GBAA2237 / Plasmid: pCRT7/C-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q81R22, dihydrofolate reductase #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-TOP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 13 % PEG 3350, 0.2M CaCl2, 0.1M MES, 1% ethanol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: May 23, 2008 / Details: Montel multilayer |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.496 |
Reflection | Resolution: 2.4→30 Å / Num. all: 59401 / Num. obs: 53699 / % possible obs: 90.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 34.6 Å2 / Rsym value: 0.088 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 4944 / Rsym value: 0.281 / % possible all: 72.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QK8 Resolution: 2.4→29.948 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.763 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 30.62 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.882 Å2 / ksol: 0.33 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.78 Å2 / Biso mean: 31.136 Å2 / Biso min: 18.69 Å2
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Refine analyze | Luzzati coordinate error obs: 0.495 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.948 Å
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Refine LS restraints |
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LS refinement shell |
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