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Yorodumi- PDB-5ett: S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ett | ||||||
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Title | S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.55 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: 1.55 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ett.cif.gz | 90.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ett.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ett.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/5ett ftp://data.pdbj.org/pub/pdb/validation_reports/et/5ett | HTTPS FTP |
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-Related structure data
Related structure data | 5etkC 5etlC 5etmC 5etnC 5etoC 5etpC 5etqSC 5etrC 5etsC 5etvC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 18304.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source 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, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase |
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-Non-polymers , 5 types, 267 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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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: 2.27 Å3/Da / Density % sol: 45.79 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.77 Details: Protein 6.9 mg/mL, 1 mM AMPCPP, 1 mM inhibitor, 0.182 MgCl2, 0.1 M tris chloride, 22%w/v PEG8000, 50 mM sodium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.0329 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0329 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→40.93 Å / Num. obs: 47134 / % possible obs: 99.3 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 2.4 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ETQ Resolution: 1.55→40.93 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 15.934 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→40.93 Å
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