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Yorodumi- PDB-5u12: E. coli dihydropteroate synthase complexed with an 8-mercaptoguan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u12 | ||||||
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Title | E. coli dihydropteroate synthase complexed with an 8-mercaptoguanine derivative: 2-azanyl-8-[(2-fluorophenyl)methylsulfanyl]-1,9-dihydropurin-6-one | ||||||
Components | Dihydropteroate synthase | ||||||
Keywords | TRANSFERASE / E. coli / DHPS / complex / pterin site | ||||||
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: 1.839 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 | 5u12.cif.gz | 121 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u12.ent.gz | 93.1 KB | Display | PDB format |
PDBx/mmJSON format | 5u12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/5u12 ftp://data.pdbj.org/pub/pdb/validation_reports/u1/5u12 | HTTPS FTP |
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-Related structure data
Related structure data | 5u0vC 5u0wC 5u0yC 5u0zC 5u10C 5u11C 5u13C 5u14C 5v79C 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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1 |
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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: 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: 2.6 Å3/Da / Density % sol: 52.76 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 0.147M magnesium acetate 27.1% [w/v] MPEG 5000 0.1M tris chloride, pH 8.8 Protein at 11.1 mg.mL-1 Cocrystallisation 1:1 (150:150 nL) reservoir:protein |
-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 315 / Detector: CCD / Date: Apr 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.839→46.57 Å / Num. obs: 54783 / % possible obs: 99.7 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.84→1.88 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.8 / CC1/2: 0.872 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AJ2 Resolution: 1.839→45.089 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.839→45.089 Å
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Refine LS restraints |
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LS refinement shell |
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