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Yorodumi- PDB-1df7: DIHYDROFOLATE REDUCTASE OF MYCOBACTERIUM TUBERCULOSIS COMPLEXED W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1df7 | ||||||
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Title | DIHYDROFOLATE REDUCTASE OF MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH NADPH AND METHOTREXATE | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / DIHYDROFOLATE REDUCTASE / STRUCTURE-BASED INHIBITOR DESIGN / FOLATEANALOGS / ROSSMANN FOLD / NICOTINAMIDE ADENINE DINUCLEOTIDE / METHOTREXATE / TUBERCULOSIS | ||||||
Function / homology | Function and homology information glycine biosynthetic process / NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Li, R. / Sirawaraporn, R. / Chitnumsub, P. / Sirawaraporn, W. / Wooden, J. / Athappilly, F. / Turley, S. / Hol, W.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Three-dimensional structure of M. tuberculosis dihydrofolate reductase reveals opportunities for the design of novel tuberculosis drugs. Authors: Li, R. / Sirawaraporn, R. / Chitnumsub, P. / Sirawaraporn, W. / Wooden, J. / Athappilly, F. / Turley, S. / Hol, W.G. #1: Journal: Biochemistry / Year: 1997 Title: Comparison of Two Independent Crystal Structures of Human Dihydrofolate Reductase Ternary Complexes Reduced with Nicotinamide Adenine Dinucleotide Phosphate and the Very Tight-Binding Inhibitor PT523 Authors: Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Rosowsky, A. / Blakley, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1df7.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1df7.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 1df7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/1df7 ftp://data.pdbj.org/pub/pdb/validation_reports/df/1df7 | 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17660.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) References: UniProt: P0A546, UniProt: P9WNX1*PLUS, dihydrofolate reductase |
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-Non-polymers , 5 types, 202 molecules
#2: Chemical | ChemComp-SO4 / | ||
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#3: Chemical | ChemComp-NDP / | ||
#4: Chemical | ChemComp-MTX / | ||
#5: Chemical | ChemComp-GOL / #6: 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: 3.05 Å3/Da / Density % sol: 59.64 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 4.5 Details: AMMONIUM SULFATE, SODIUM ACETATE, GLYCEROL, NADPH, METHOTREXATE, POTASSIUM PHOSPHATE, DTT, POTASSIUM CHLORIDE, pH 4.5, VAPOR DIFFUSION, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0188 |
Detector | Type: SBC-2 / Detector: CCD / Date: Sep 17, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0188 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 23394 / Num. obs: 109952 / % possible obs: 99.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.7→1.78 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.263 / % possible all: 99.7 |
Reflection | *PLUS Num. obs: 23394 / Num. measured all: 109952 |
Reflection shell | *PLUS % possible obs: 99.7 % |
-Processing
Software |
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Refinement | Resolution: 1.7→50 Å / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |