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Yorodumi- PDB-6pbo: Staphylococcus aureus Dihydrofolate reductase in complex with NAD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pbo | ||||||
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Title | Staphylococcus aureus Dihydrofolate reductase in complex with NADPH and UCP1232 | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | ANTIMICROBIAL PROTEIN / DHFR / methotrexate / antifolate / NADPH | ||||||
Function / homology | Function and homology information dihydrofolate metabolic 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.649 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 | 6pbo.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pbo.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 6pbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pbo_validation.pdf.gz | 515.2 KB | Display | wwPDB validaton report |
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Full document | 6pbo_full_validation.pdf.gz | 520.8 KB | Display | |
Data in XML | 6pbo_validation.xml.gz | 2.7 KB | Display | |
Data in CIF | 6pbo_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/6pbo ftp://data.pdbj.org/pub/pdb/validation_reports/pb/6pbo | HTTPS FTP |
-Related structure data
Related structure data | 6p9zC 3f0qS C: citing same article (ref.) 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: 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A017, dihydrofolate reductase |
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#2: Chemical | ChemComp-O71 / ( |
#3: Chemical | ChemComp-XNP / |
#4: Chemical | ChemComp-NAP / |
#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: 2.7 Å3/Da / Density % sol: 54.49 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop Details: 0.1 MES, pH 6.0, 0.1M sodium acetate, 15% PEG 10K and 20% gamma-butyrolactone |
-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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2017 |
Radiation | Monochromator: 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: 1.649→39.47 Å / Num. obs: 23971 / % possible obs: 97.07 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.649→1.708 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.658 / Num. unique obs: 2394 / % possible all: 99.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F0Q Resolution: 1.649→39.47 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.649→39.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.649→1.6903 Å
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