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Yorodumi- PDB-7t7q: R-27 In Complex with S. aureus DHFR and alpha-NADPH - Remediated ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t7q | ||||||||||||
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Title | R-27 In Complex with S. aureus DHFR and alpha-NADPH - Remediated for comparison with tNADPH | ||||||||||||
Components | Dihydrofolate reductase | ||||||||||||
Keywords | OXIDOREDUCTASE / DHFR / cofactor / Antibiotic resistance / Antifolates | ||||||||||||
Function / homology | Function and homology information 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 | Staphylococcus aureus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||
Authors | Reeve, S.M. / Wang, S. / Donald, B.R. / Wright, D.L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Plos Comput.Biol. / Year: 2022 Title: Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus. Authors: Wang, S. / Reeve, S.M. / Holt, G.T. / Ojewole, A.A. / Frenkel, M.S. / Gainza, P. / Keshipeddy, S. / Fowler, V.G. / Wright, D.L. / Donald, B.R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t7q.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t7q.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 7t7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t7q_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7t7q_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7t7q_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 7t7q_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/7t7q ftp://data.pdbj.org/pub/pdb/validation_reports/t7/7t7q | HTTPS FTP |
-Related structure data
Related structure data | 7t7sC 3f0qS 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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-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 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A017, dihydrofolate reductase |
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#2: Chemical | ChemComp-NDW / |
#3: Chemical | ChemComp-06U / |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1M MES pH 6.25, 0.1M Sodium Acetate, 13% PEG 10,000, 0.5% gamma-Butrylactone |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→31.88 Å / Num. obs: 10390 / % possible obs: 97.95 % / Redundancy: 18.2 % / Biso Wilson estimate: 38.15 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 20.81 |
Reflection shell | Resolution: 2.2→2.42 Å / Rmerge(I) obs: 0.9 / Num. unique obs: 866 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F0Q Resolution: 2.2→31.846 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.26 / 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: 2.2→31.846 Å
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Refine LS restraints |
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LS refinement shell |
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