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Yorodumi- PDB-4xe6: Staphylococcus aureus Dihydrofolate Reductase complexed with NADP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xe6 | ||||||
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Title | Staphylococcus aureus Dihydrofolate Reductase complexed with NADPH and 6-ETHYL-5-[(3R)-3-[3-METHOXY-5-(PYRIDIN-4-YL)PHENYL]BUT-1-YN-1-YL]PYRIMIDINE-2,4-DIAMINE (UCP1061) | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE Inhibitor / Dihydrofolate reductase / Oxidoreductase / Methicillin-resistant Staphylococcus aureus / Antifolates / Enantiopure Inhibitors / OXIDOREDUCTASE-OXIDOREDUCTASE Inhibitor complex | ||||||
Function / homology | Function and homology information glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.692 Å | ||||||
Authors | Reeve, S.M. / Anderson, A.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Stereo-selectively Induced Cofactor Switching Provides Insight into Cofactor Site Plasticity as a Possible Mechanism of Antifolate Resistance Authors: Keshipeddy, S. / Reeve, S.M. / Anderson, A.C. / Wright, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xe6.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xe6.ent.gz | 34.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xe6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/4xe6 ftp://data.pdbj.org/pub/pdb/validation_reports/xe/4xe6 | HTTPS FTP |
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-Related structure data
Related structure data | 3f0qS S: Starting model for refinement |
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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: 18389.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folA / Plasmid: pET-41a(+) / Details (production host): Expression Vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P0A017, dihydrofolate reductase |
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#2: Chemical | ChemComp-06U / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-NDP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: 0.1M MES pH 6.25, 0.1M Sodium Acetate, 13% PEG 10,000, 0.5% gamma-butrylactone Temp details: Cold Room |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2014 |
Radiation | Monochromator: Si(111) Double Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→31.877 Å / Num. obs: 5929 / % possible obs: 99.6 % / Redundancy: 18.2 % / Biso Wilson estimate: 36.19 Å2 / Rsym value: 0.16 / Net I/σ(I): 38.6 |
Reflection shell | Resolution: 2.69→2.74 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 9 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F0Q Resolution: 2.692→31.877 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.26 / 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: 2.692→31.877 Å
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Refine LS restraints |
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LS refinement shell |
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