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Yorodumi- PDB-4cwb: Staphylococcus aureus 7,8-Dihydro-6-hydroxymethylpterin- pyrophos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cwb | ||||||
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Title | Staphylococcus aureus 7,8-Dihydro-6-hydroxymethylpterin- pyrophosphokinase in complex with AMPCPP and an inhibitor | ||||||
Components | 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE | ||||||
Keywords | TRANSFERASE / 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 / NITRATE ION / Chem-X6L / : Function and homology information | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cwb.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cwb.ent.gz | 37.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/4cwb ftp://data.pdbj.org/pub/pdb/validation_reports/cw/4cwb | HTTPS FTP |
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-Related structure data
Related structure data | 4crjC 4cyuC 4ad6S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18304.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: C8MLE4, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase |
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-Non-polymers , 5 types, 146 molecules
#2: Chemical | #3: Chemical | ChemComp-APC / | #4: Chemical | ChemComp-NO3 / | #5: Chemical | ChemComp-X6L / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | HEXAHISTID |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.1 % / Description: NONE |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PROTEIN 6.9 MG/ML 1 MM AMPCPP, 1 MM INHIBITOR, 2 MM MAGNESIUM CHLORIDE, AMMONIUM NITRATE 0.275 M, PEG3350 22.2% W/V, SITTING DROP, 281 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→42.29 Å / Num. obs: 29793 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.56→1.58 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.7 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AD6 Resolution: 1.56→42.33 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.162 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. AN ALTERNATE CONFORMATION OF THE LOOP 3 RESIDUE LYS86 IS SUGGESTED, THIS WAS NOT MODELLED DUE TO POOR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. AN ALTERNATE CONFORMATION OF THE LOOP 3 RESIDUE LYS86 IS SUGGESTED, THIS WAS NOT MODELLED DUE TO POOR DENSITY. THE TERMINAL RESIDUE LYS158 IS SUGGESTED TO ADOPT MULTIPLE CONFORMATIONS. ONLY THE PREDOMINANT CONFORMATION IS MODELLED DUE TO ELSEWISE POOR DENSITY.
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.534 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→42.33 Å
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Refine LS restraints |
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