[English] 日本語
Yorodumi- PDB-4cyu: Staphylococcus aureus 7,8-Dihydro-6-hydroxymethylpterin- pyrophos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cyu | ||||||
---|---|---|---|---|---|---|---|
Title | Staphylococcus aureus 7,8-Dihydro-6-hydroxymethylpterin- pyrophosphokinase in complex with AMPCPP | ||||||
Components | (7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN- ...) x 2 | ||||||
Keywords | TRANSFERASE / S.AUREUS / FOLATE / STRUCTURE-BASED DRUG DESIGN | ||||||
Function / homology | 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : Function and homology information | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Dennis, M.L. / Swarbrick, J.D. / Peat, T.S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Structure-Based Design and Development of Functionalized Mercaptoguanine Derivatives as Inhibitors of the Folate Biosynthesis Pathway Enzyme 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase ...Title: Structure-Based Design and Development of Functionalized Mercaptoguanine Derivatives as Inhibitors of the Folate Biosynthesis Pathway Enzyme 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase from Staphylococcus Aureus. Authors: Dennis, M.L. / Chhabra, S. / Wang, Z. / Debono, A. / Dolezal, O. / Newman, J. / Pitcher, N.P. / Rahmani, R. / Cleary, B. / Barlow, N. / Hattarki, M. / Graham, B. / Peat, T.S. / Baell, J.B. / Swarbrick, J.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4cyu.cif.gz | 144.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4cyu.ent.gz | 113.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/4cyu ftp://data.pdbj.org/pub/pdb/validation_reports/cy/4cyu | HTTPS FTP |
---|
-Related structure data
Related structure data | 4crjC 4cwbC 4ad6S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
-7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN- ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 18303.111 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: C8MLE4, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase |
---|---|
#2: Protein | Mass: 18304.098 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: C8MLE4, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase |
-Non-polymers , 4 types, 27 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-APC / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | HEXAHISTID |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.62 % / Description: NONE |
---|---|
Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PROTEIN 6.9 MG/ML 1 MM AMPCPP, 2 MM MAGNESIUM CHLORIDE, MAGNESIUM ACETATE 0.119 M, PEG8000 12.6% W/V, TRIS CHLORIDE 0.12 M, SITTING DROP, 281 K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.008 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→45.53 Å / Num. obs: 18506 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.7→2.83 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AD6 Resolution: 2.7→45.53 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY RESIDUES OF LOOP 2 ARE NOT MODELLED IN CHAINS A (RESIDUES 45-48) AND B (RESIDUES 46-48) DUE TO POOR DENSITY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.203 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→45.53 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|