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Yorodumi- PDB-6prd: S. aureus dihydrofolate reductase co-crystallized with para-metho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6prd | ||||||
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Title | S. aureus dihydrofolate reductase co-crystallized with para-methoxyphenyl-dimethyoxydihydropthalazine inhibitor and NADP(H) | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / DIHYDROFOLATE REDUCTASE / OXIDOREDUCTASE-INHIBITOR complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Bourne, C.R. / Thomas, L.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2020 Title: Inhibitor design to target a unique feature in the folate pocket of Staphylococcus aureus dihydrofolate reductase. Authors: Muddala, N.P. / White, J.C. / Nammalwar, B. / Pratt, I. / Thomas, L.M. / Bunce, R.A. / Berlin, K.D. / Bourne, C.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6prd.cif.gz | 56.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6prd.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 6prd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6prd_validation.pdf.gz | 437.1 KB | Display | wwPDB validaton report |
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Full document | 6prd_full_validation.pdf.gz | 442.2 KB | Display | |
Data in XML | 6prd_validation.xml.gz | 2.6 KB | Display | |
Data in CIF | 6prd_validation.cif.gz | 5.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/6prd ftp://data.pdbj.org/pub/pdb/validation_reports/pr/6prd | HTTPS FTP |
-Related structure data
Related structure data | 6pr6C 6pr7C 6pr8C 6pr9C 6praC 6prbC 3m08S 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: 18611.336 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 | #3: Chemical | ChemComp-OWG / | #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: 2.56 Å3/Da / Density % sol: 51.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 20%PEG6000, 0.1M MES, 0.15M Na Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 23, 2015 / Details: VeriMax HF |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→41.8 Å / Num. obs: 13335 / % possible obs: 98 % / Redundancy: 8.9 % / Biso Wilson estimate: 25.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.01→2.04 Å / Rmerge(I) obs: 0.167 / Num. unique obs: 612 / CC1/2: 0.989 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3M08 Resolution: 2.01→41.79 Å / FOM work R set: 0.8217 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.18 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.64 Å2 / Biso mean: 28.23 Å2 / Biso min: 11.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.01→41.79 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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