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Yorodumi- PDB-3qbc: Structure and design of a new pterin site inhibitor of S. aureus HPPK -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qbc | ||||||
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Title | Structure and design of a new pterin site inhibitor of S. aureus HPPK | ||||||
Components | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase | ||||||
Keywords | Transferase/Transferase inhibitor / protein-inhibitor complex / ferredoxin-like fold / kinase / ATP binding / 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 / ATP binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Peat, T.S. / Chhabra, S. / Swarbrick, J.D. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Structure of S. aureus HPPK and the discovery of a new substrate site inhibitor Authors: Chhabra, S. / Dolezal, O. / Collins, B.M. / Newman, J. / Simpson, J.S. / Macreadie, I.G. / Fernley, R. / Peat, T.S. / Swarbrick, J.D. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Crystallization and preliminary X-ray analysis of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase from Staphylococcus aureus Authors: Chhabra, S. / Newman, J. / Peat, T.S. / Fernley, R.T. / Caine, J. / Simpson, J.S. / 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 | 3qbc.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qbc.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 3qbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qbc_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 3qbc_full_validation.pdf.gz | 461.5 KB | Display | |
Data in XML | 3qbc_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 3qbc_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/3qbc ftp://data.pdbj.org/pub/pdb/validation_reports/qb/3qbc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 18304.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) References: UniProt: Q99W87, UniProt: A0A0H3JXR3*PLUS, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase #2: Chemical | #3: 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: 1.95 Å3/Da / Density % sol: 36.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 90mM bis-tris(pH 6.5), 10mM sodium acetate(pH 4.6), 175mM sodium formate, 1.08M sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.955 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 16, 2009 | |||||||||||||||||||||
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.955 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.65→50.7 Å / Num. all: 33864 / Num. obs: 33864 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.11 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RAO, 1CBK Resolution: 1.65→42.3 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.125 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.115 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.696 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→42.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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