+Open data
-Basic information
Entry | Database: PDB / ID: 8ap0 | ||||||
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Title | ForT Mutant T138V | ||||||
Components | Beta-ribofuranosylaminobenzene 5'-phosphate synthase | ||||||
Keywords | STRUCTURAL PROTEIN / Formycin Biosynthesis pathway protein C-nucleoside formation enzyme | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces kaniharaensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Li, W. / Naismith, J.H. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Open Biology / Year: 2023 Title: Experimental and computational snapshots of C-C bond formation in a C-nucleoside synthase. Authors: Li, W. / Girt, G.C. / Radadiya, A. / Stewart, J.J.P. / Richards, N.G.J. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ap0.cif.gz | 153 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ap0.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ap0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ap0_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ap0_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ap0_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 8ap0_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/8ap0 ftp://data.pdbj.org/pub/pdb/validation_reports/ap/8ap0 | HTTPS FTP |
-Related structure data
Related structure data | 8aozC 6yqqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules AAA
#1: Protein | Mass: 36625.352 Da / Num. of mol.: 1 / Mutation: T138V Source method: isolated from a genetically manipulated source Details: Genetically mutated T138V / Source: (gene. exp.) Streptomyces kaniharaensis (bacteria) / Gene: cof6, F7Q99_03185 / Plasmid: pHis-TEV / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): BL21(DE3) pLysE / References: UniProt: A0A5S9CYM0 |
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#2: Sugar | ChemComp-PRP / |
-Non-polymers , 5 types, 315 molecules
#3: Chemical | ChemComp-MYO / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-K / | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 3.45 Å3/Da / Density % sol: 54.37 % / Description: Long needle shape crystal |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Bis-Tris Propane [20mM] pH7.0, Glycerol [20%], PEG 8000 [16%], Monopotassium phosphate [40mM] Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cooled by liquid Nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→60 Å / Num. obs: 63680 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 1 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 4624 / CC1/2: 0.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YQQ Resolution: 1.6→59.865 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / SU B: 6.61 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.071 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.414 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→59.865 Å
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Refine LS restraints |
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LS refinement shell |
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