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Yorodumi- PDB-6flf: Deoxyguanylosuccinate synthase (DgsS) structure at 1.33 Angstrom ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6flf | ||||||
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Title | Deoxyguanylosuccinate synthase (DgsS) structure at 1.33 Angstrom resolution. | ||||||
Components | Adenylosuccinate synthetaseAdenylosuccinate synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / 2 / 6-diaminopurine / phage phiVC8 / Synthetase | ||||||
Function / homology | Function and homology information 2-amino-2'-deoxyadenylo-succinate synthase / adenylosuccinate synthase activity / purine nucleotide biosynthetic process / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Vibrio phage phiVC8 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||
Authors | Sleiman, D. / Loc'h, J. / Haouz, A. / Kaminski, P.A. | ||||||
Citation | Journal: Science / Year: 2021 Title: A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes. Authors: Sleiman, D. / Garcia, P.S. / Lagune, M. / Loc'h, J. / Haouz, A. / Taib, N. / Rothlisberger, P. / Gribaldo, S. / Marliere, P. / Kaminski, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6flf.cif.gz | 140.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6flf.ent.gz | 107.6 KB | Display | PDB format |
PDBx/mmJSON format | 6flf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/6flf ftp://data.pdbj.org/pub/pdb/validation_reports/fl/6flf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 40392.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio phage phiVC8 (virus) / Gene: phiVC8_p27 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G3FFN6 |
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#2: 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: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2M NaCl 12% PEG 6K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→49.4 Å / Num. obs: 88372 / % possible obs: 99.2 % / Redundancy: 4.74 % / Biso Wilson estimate: 23.56 Å2 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.33→1.41 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→49.4 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.052 / SU Rfree Blow DPI: 0.055 / SU Rfree Cruickshank DPI: 0.053
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Displacement parameters | Biso mean: 29.94 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.33→49.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.33→1.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 3.6476 Å / Origin y: 15.1999 Å / Origin z: 14.1167 Å
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Refinement TLS group | Selection details: { A|* } |