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Yorodumi- PDB-5hf2: Staphylococcus aureus Dihydrofolate Reductase complexed with cycl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hf2 | ||||||
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Title | Staphylococcus aureus Dihydrofolate Reductase complexed with cyclized alpha-NADPH anomer and 3'-(3-(2,4-diamino-6-ethylpyrimidin-5-yl)prop-2-yn-1-yl)-5'-methoxy-[1,1'-biphenyl]-4-carboxylic acid (UCP1175) | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / NADPH / Propargyl-linked antifolates / Dihydrofolate Reductase / Antibiotics | ||||||
Function / homology | Function and homology information dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.81 Å | ||||||
Authors | Reeve, S.M. / Anderson, A.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Staphylococcus aureus Dihydrofolate Reductase complexed with cyclized alpha-NADPH anomer and 3'-(3-(2,4-diamino-6-ethylpyrimidin-5-yl)prop-2-yn-1-yl)-5'-methoxy-[1,1'-biphenyl]-4-carboxylic acid (UCP1175) Authors: Reeve, S.M. / Anderson, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hf2.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hf2.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 5hf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/5hf2 ftp://data.pdbj.org/pub/pdb/validation_reports/hf/5hf2 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 18015.557 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folA / Plasmid: pET-41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A017, dihydrofolate reductase |
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#2: Chemical | ChemComp-XNP / |
#3: Chemical | ChemComp-U75 / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M MES pH 5.0, 0.1M Sodium acetate, 17% PEG 10,000 and 1% gamma-butyrolactone |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5417 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→25.17 Å / Num. obs: 18798 / % possible obs: 99.9 % / Redundancy: 12.32 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.81→1.87 Å / Redundancy: 12.03 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Resolution: 1.81→25.166 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→25.166 Å
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Refine LS restraints |
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LS refinement shell |
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