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Yorodumi- PDB-5v79: E. coli dihydropteroate synthase complexed with an 8-mercaptoguan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v79 | ||||||
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Title | E. coli dihydropteroate synthase complexed with an 8-mercaptoguanine derivative: 2-((2-amino-9-methyl-6-oxo-6,9-dihydro-1H-purin-8-yl)thio)-N-phenylacetamide | ||||||
Components | Dihydropteroate synthase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / DHPS / complex / pterin site / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli O6:H1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Dennis, M.L. / Peat, T.S. / Swarbrick, J.D. | ||||||
Citation | Journal: Chemistry / Year: 2018 Title: 8-Mercaptoguanine Derivatives as Inhibitors of Dihydropteroate Synthase. Authors: Dennis, M.L. / Lee, M.D. / Harjani, J.R. / Ahmed, M. / DeBono, A.J. / Pitcher, N.P. / Wang, Z.C. / Chhabra, S. / Barlow, N. / Rahmani, R. / Cleary, B. / Dolezal, O. / Hattarki, M. / Aurelio, ...Authors: Dennis, M.L. / Lee, M.D. / Harjani, J.R. / Ahmed, M. / DeBono, A.J. / Pitcher, N.P. / Wang, Z.C. / Chhabra, S. / Barlow, N. / Rahmani, R. / Cleary, B. / Dolezal, O. / Hattarki, M. / Aurelio, L. / Shonberg, J. / 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 | 5v79.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v79.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 5v79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v79_validation.pdf.gz | 951.4 KB | Display | wwPDB validaton report |
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Full document | 5v79_full_validation.pdf.gz | 953.1 KB | Display | |
Data in XML | 5v79_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 5v79_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/5v79 ftp://data.pdbj.org/pub/pdb/validation_reports/v7/5v79 | HTTPS FTP |
-Related structure data
Related structure data | 5u0vC 5u0wC 5u0yC 5u0zC 5u10C 5u11C 5u12C 5u13C 5u14C 5v7aC 1aj2S 5u0x 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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Unit cell |
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-Components
#1: Protein | Mass: 30796.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria) Strain: CFT073 / ATCC 700928 / UPEC / Gene: folP, c3933 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AC14, dihydropteroate synthase #2: Chemical | #3: Chemical | #4: 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: 2.62 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 0.248 M magnesium nitrate 20.3 %(w/v) PEG 8000 0.1 M tris chloride, pH 8.8 Protein at 11.1 mg.mL-1 1:1 (150:150 nL) reservoir:protein Ligand soaked into crystal (~4 h, ~2 mM) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→46.3 Å / Num. obs: 29678 / % possible obs: 98.4 % / Redundancy: 6.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.082 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.25→2.32 Å / Redundancy: 7.32 % / Rmerge(I) obs: 1.112 / Mean I/σ(I) obs: 2.8 / Num. measured obs: 2754 / CC1/2: 0.865 / Rpim(I) all: 0.447 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AJ2 Resolution: 2.25→46.3 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.205 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.806 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→46.3 Å
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Refine LS restraints |
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