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Yorodumi- PDB-6p9z: Staphylococcus aureus Dihydrofolate reductase in complex with NAD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p9z | ||||||
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Title | Staphylococcus aureus Dihydrofolate reductase in complex with NADPH and Methotrexate | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | antimicrobial protein / oxidoreductase / DHFR / methotrexate / antifolate / NADPH | ||||||
Function / homology | Function and homology information dihydrofolate metabolic process / glycine biosynthetic 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: 1.86 Å | ||||||
Authors | Reeve, S.M. / Wright, D.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2019 Title: Toward Broad Spectrum Dihydrofolate Reductase Inhibitors Targeting Trimethoprim Resistant Enzymes Identified in Clinical Isolates of Methicillin ResistantStaphylococcus aureus. Authors: Reeve, S.M. / Si, D. / Krucinska, J. / Yan, Y. / Viswanathan, K. / Wang, S. / Holt, G.T. / Frenkel, M.S. / Ojewole, A.A. / Estrada, A. / Agabiti, S.S. / Alverson, J.B. / Gibson, N.D. / ...Authors: Reeve, S.M. / Si, D. / Krucinska, J. / Yan, Y. / Viswanathan, K. / Wang, S. / Holt, G.T. / Frenkel, M.S. / Ojewole, A.A. / Estrada, A. / Agabiti, S.S. / Alverson, J.B. / Gibson, N.D. / Priestley, N.D. / Wiemer, A.J. / Donald, B.R. / 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 | 6p9z.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p9z.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 6p9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p9z_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6p9z_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6p9z_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 6p9z_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/6p9z ftp://data.pdbj.org/pub/pdb/validation_reports/p9/6p9z | HTTPS FTP |
-Related structure data
Related structure data | 6pboC 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 / Plasmid: pET-41a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A017, dihydrofolate reductase |
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#2: Chemical | ChemComp-MTX / |
#3: Chemical | ChemComp-NAP / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.94 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M MES, pH 5.5 0.2 M sodium acetate 15% PEG 10,000 20% gamma-butyrolactone, additive Temp details: Cold room |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.95 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 15, 2017 / Details: image plate |
Radiation | Monochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→32.11 Å / Num. obs: 17420 / % possible obs: 99.28 % / Redundancy: 14.1 % / Net I/σ(I): 40.8 |
Reflection shell | Resolution: 1.86→1.92 Å / Num. unique obs: 1689 / % possible all: 98.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F0Q Resolution: 1.86→32.11 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→32.11 Å
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Refine LS restraints |
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LS refinement shell |
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