[English] 日本語
Yorodumi- PDB-6prb: S. aureus dihydrofolate reductase co-crystallized with cyclopropy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6prb | ||||||
---|---|---|---|---|---|---|---|
Title | S. aureus dihydrofolate reductase co-crystallized with cyclopropyl-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 Å | ||||||
Authors | Bourne, C.R. / Thomas, L.M. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6prb.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6prb.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 6prb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6prb_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6prb_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6prb_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 6prb_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/6prb ftp://data.pdbj.org/pub/pdb/validation_reports/pr/6prb | HTTPS FTP |
-Related structure data
Related structure data | 6pr6C 6pr7C 6pr8C 6pr9C 6praC 6prdC 3m08S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#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 |
---|
-Non-polymers , 5 types, 132 molecules
#2: Chemical | ChemComp-R0Y / ( |
---|---|
#3: Chemical | ChemComp-OWM / ( |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-NAP / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 20, 2015 |
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→41.9 Å / Num. obs: 13803 / % possible obs: 96.9 % / Redundancy: 14.4 % / Biso Wilson estimate: 27.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Net I/σ(I): 37.2 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.482 / Num. unique obs: 675 / CC1/2: 0.973 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3M08 Resolution: 2→41.83 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.4 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→41.83 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|