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Yorodumi- PDB-5etm: E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5etm | ||||||
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Title | E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.46 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 / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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 | 5etm.cif.gz | 54.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5etm.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 5etm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5etm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5etm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5etm_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 5etm_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/5etm ftp://data.pdbj.org/pub/pdb/validation_reports/et/5etm | HTTPS FTP |
-Related structure data
Related structure data | 5etkSC 5etlC 5etnC 5etoC 5etpC 5etqC 5etrC 5etsC 5ettC 5etvC 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: 18312.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folK, b0142, JW0138 / Production host: Escherichia coli (E. coli) References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase |
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-Non-polymers , 6 types, 96 molecules
#2: Chemical | ChemComp-5RW / | ||||||
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#3: Chemical | ChemComp-APC / | ||||||
#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.55 Details: Protein 6.6 mg/mL, 1 mM AMPCPP, 1 mM inhibitor, 2 mM Magnesium Chloride, 27.5 %w/v PEG4000, 0.1 M sodium HEPES, 0.196 M Calcium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→34.67 Å / Num. obs: 24472 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.46→1.48 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ETK Resolution: 1.46→34.67 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.089 / 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: 12.946 Å2
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Refinement step | Cycle: 1 / Resolution: 1.46→34.67 Å
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