[English] 日本語
Yorodumi- PDB-5etq: S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5etq | ||||||
---|---|---|---|---|---|---|---|
Title | S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.96 angstrom resolution | ||||||
Components | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE inhibitor / inhibitor / complex / ampcpp / pyrophosphokinase / TRANSFERASE-TRANSFERASE inhibitor complex | ||||||
Function / homology | Function and homology information 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Dennis, M.L. / Peat, T.S. / Swarbrick, J.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Structural Basis for the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase from Staphylococcus aureus and Escherichia coli. Authors: Dennis, M.L. / Pitcher, N.P. / Lee, M.D. / DeBono, A.J. / Wang, Z.C. / Harjani, J.R. / Rahmani, R. / Cleary, B. / Peat, T.S. / Baell, J.B. / Swarbrick, J.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5etq.cif.gz | 87.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5etq.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 5etq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/5etq ftp://data.pdbj.org/pub/pdb/validation_reports/et/5etq | HTTPS FTP |
---|
-Related structure data
Related structure data | 5etkC 5etlC 5etmC 5etnC 5etoC 5etpC 5etrC 5etsC 5ettC 5etvC 4cwbS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18320.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Additional density was noted at residue Cys80 in both protomers of the asymmetric unit. This was modelled as the oxidized form, S-hydroxy cysteine. Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: RK60_02090, RK67_01645, RK72_06915, RK74_04210, RK75_00240, RK80_01970, RK83_05435, RK84_03130, RK95_04415, RK96_04825, RK98_03440, RK99_07885, RL05_10010, RL06_09555, RL08_05305, TM59_02255 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H1ZSM1, UniProt: Q2G0Q5*PLUS |
---|
-Non-polymers , 5 types, 147 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.36 % |
---|---|
Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PROTEIN 6.9 MG/ML, 1 MM AMPCPP, 1 MM INHIBITOR, 0.202 M MAGNESIUM CHLORIDE, 0.1 M TRIS CHLORIDE, 20%w/v PEG8000, 50 MM SODIUM THIOCYANATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9707 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9707 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→68.2 Å / Num. obs: 23517 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.96→2.01 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CWB Resolution: 1.96→50.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.433 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→50.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|