+Open data
-Basic information
Entry | Database: PDB / ID: 2rk2 | ||||||
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Title | DHFR R-67 complexed with NADP | ||||||
Components | Dihydrofolate reductase type 2 | ||||||
Keywords | OXIDOREDUCTASE / NADP / asymmetric ligand binding / Antibiotic resistance / Methotrexate resistance / One-carbon metabolism / Trimethoprim resistance | ||||||
Function / homology | Function and homology information response to methotrexate / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / response to xenobiotic stimulus / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Krahn, J.M. / London, R.E. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Crystal structure of a type II dihydrofolate reductase catalytic ternary complex. Authors: Krahn, J.M. / Jackson, M.R. / DeRose, E.F. / Howell, E.E. / London, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rk2.cif.gz | 31.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rk2.ent.gz | 20.2 KB | Display | PDB format |
PDBx/mmJSON format | 2rk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/2rk2 ftp://data.pdbj.org/pub/pdb/validation_reports/rk/2rk2 | HTTPS FTP |
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-Related structure data
Related structure data | 2rh2SC 2rk1C 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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Details | The biological assembly is a tetramer generated from the monomer in the asymmetric unit with the symmetry operations: x, y, z; y, x, -z; -x, -y, z; -y, -x, -z; The NADP ligand should be included only for the identity operator, and assigned full occupancy. Water molecules that clash with NADP should then be removed to obtain the set of waters that are valid for the tetramer. Tyr69 and Gln67 are also asymmetric, but the correlation of their alternate conformations to the asymmetric ligand binding has not been conclusively determined. |
-Components
#1: Protein | Mass: 6732.528 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) Strain: TMP-RESISTANT, CONTAINING R67 DHFR OVERPRODUCING PLASMID PLZ1 References: UniProt: P00383, dihydrofolate reductase | ||
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#2: Chemical | ChemComp-NAP / | ||
#3: Chemical | #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: 2.2 Å3/Da / Density % sol: 44.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50% 2-methyl-2,4-pentanediol (MPD), 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Jul 30, 2007 / Details: Varimax HF, Confocal mirrors |
Radiation | Monochromator: Confocal mirrors (Varimax HF) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 4883 / Num. obs: 4883 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 4.5 / Num. unique all: 396 / % possible all: 83.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RH2 Resolution: 1.9→22.86 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.928 / SU ML: 0.087 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Partial occupancies are estimates, and were not refined.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.783 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→22.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.933 Å / Total num. of bins used: 30
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