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Yorodumi- PDB-3dau: Crystal structure of the ternary MTX NADPH complex of Escherichia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dau | ||||||
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Title | Crystal structure of the ternary MTX NADPH complex of Escherichia coli dihydrofolate reductase | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / pseudo-Rossmann fold / adenine nucleotide binding domain / Antibiotic resistance / Methotrexate resistance / NADP / One-carbon metabolism / Trimethoprim resistance | ||||||
Function / homology | Function and homology information methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dau.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dau.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/3dau ftp://data.pdbj.org/pub/pdb/validation_reports/da/3dau | HTTPS FTP |
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-Related structure data
Related structure data | 3datC 1rh3S S: Starting model for refinement 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: 18019.340 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.) Escherichia coli (E. coli) / Strain: K12 / Gene: folA, tmrA, b0048, JW0047 / Plasmid: Champion pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ABQ4, dihydrofolate reductase |
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#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 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.67 % |
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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 NaCl, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2005 / Details: Bent conical mirror |
Radiation | Monochromator: Bent Germanium (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→20 Å / Num. all: 55916 / Num. obs: 50833 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Rmerge(I) obs: 0.059 / Χ2: 1.464 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.921 / Mean I/σ(I) obs: 1.24 / Num. unique all: 5001 / Χ2: 1.458 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1RH3 Resolution: 1.5→18.88 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.203 / SU ML: 0.037 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.064 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 26.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→18.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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