+Open data
-Basic information
Entry | Database: PDB / ID: 2rh2 | ||||||
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Title | High Resolution DHFR R-67 | ||||||
Components | Dihydrofolate reductase type 2 | ||||||
Keywords | OXIDOREDUCTASE / FOLATE METABOLISM / PLASMID-ENCODED R67 DHFR / TMP-RESISTANT DHFR / Antibiotic resistance / Methotrexate resistance / NADP / 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: 0.96 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 | 2rh2.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rh2.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 2rh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/2rh2 ftp://data.pdbj.org/pub/pdb/validation_reports/rh/2rh2 | HTTPS FTP |
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-Related structure data
Related structure data | 2rk1C 2rk2C 1vieS 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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2 |
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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 by the operations: x, y, z; y, x, -z; -x, -y, z; -y, -x, z; |
-Components
#1: Protein | Mass: 6732.528 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Description: TMP-RESISTANT, CONTAINING R67 DHFR OVERPRODUCING PLASMID PLZ1 Production host: Escherichia coli (E. coli) / References: UniProt: P00383, dihydrofolate reductase | ||
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#2: Chemical | ChemComp-MRD / ( #3: 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: 2.22 Å3/Da / Density % sol: 44.55 % |
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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 at 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: Apr 15, 2007 / Details: Osmic VariMax HF confocal mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 0.96→25 Å / Num. all: 32858 / Num. obs: 32858 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 16.3 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 0.96→0.99 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3331 / Rsym value: 0.657 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VIE Resolution: 0.96→25 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.985 / SU B: 0.383 / SU ML: 0.01 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.017 / ESU R Free: 0.017 / Stereochemistry target values: Engh & Huber / Details: All protein hydrogens are included.
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.397 Å2
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Refinement step | Cycle: LAST / Resolution: 0.96→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.96→0.985 Å / Total num. of bins used: 20
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