[English] 日本語
Yorodumi- PDB-3dat: Crystal structure of the ternary MTX NADPH complex of Bacillus an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dat | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the ternary MTX NADPH complex of Bacillus anthracis dihydrofolate reductase | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / dual-site inhibition / pseudo-Rossmann fold / adenine nucleotide binding domain | ||||||
Function / homology | Function and homology information dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus anthracis str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Bennett, B.C. / Dealwis, C.G. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2009 Title: X-ray structure of the ternary MTX.NADPH complex of the anthrax dihydrofolate reductase: a pharmacophore for dual-site inhibitor design. Authors: Bennett, B.C. / Wan, Q. / Ahmad, M.F. / Langan, P. / Dealwis, C.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3dat.cif.gz | 50.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3dat.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/3dat ftp://data.pdbj.org/pub/pdb/validation_reports/da/3dat | HTTPS FTP |
---|
-Related structure data
Related structure data | 3dauC 2qk8S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 19148.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: A 6xHis tag and a SUMO protein were fused to the N-terminus of the target protein. This is removed prior to crystallization with the SUMO protease (Ulp1). Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Strain: Sterne / Gene: dfrA, BAS2083, BA_2237, GBAA2237 / Plasmid: Champion pET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81R22, dihydrofolate reductase |
---|---|
#2: Chemical | ChemComp-MTX / |
#3: Chemical | ChemComp-NDP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.96 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-Tris pH 5.5, 0.2 M CaCl2, 20% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 4, 2008 / Details: Mirrors |
Radiation | Monochromator: Silicon (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 10216 / % possible obs: 93.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.131 / Χ2: 1.923 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3 / Num. unique all: 823 / Χ2: 2.033 / % possible all: 73.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2QK8 Resolution: 2.3→15.31 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.889 / SU B: 16.885 / SU ML: 0.235 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.42 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 44.502 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→15.31 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.358 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -8.3642 Å / Origin y: -9.1675 Å / Origin z: 14.223 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|