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Yorodumi- PDB-6tnh: Deoxyguanylosuccinate synthase (DgsS) quaternary structure with A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tnh | ||||||
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Title | Deoxyguanylosuccinate synthase (DgsS) quaternary structure with AMPPcP, dGMP, Asp, Magnesium at 2.21 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: 2.21 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 | 6tnh.cif.gz | 288.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tnh.ent.gz | 231 KB | Display | PDB format |
PDBx/mmJSON format | 6tnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/6tnh ftp://data.pdbj.org/pub/pdb/validation_reports/tn/6tnh | HTTPS FTP |
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-Related structure data
Related structure data | 6flfSC 6fm0C 6fm1C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40597.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio phage phiVC8 (virus) / Gene: phiVC8_p27 / Production host: Escherichia coli (E. coli) / References: UniProt: G3FFN6 |
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-Non-polymers , 6 types, 406 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ASP / | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-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: 2.46 Å3/Da / Density % sol: 50.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1M LiSO4, 2%PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979346 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979346 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→47.38 Å / Num. obs: 40942 / % possible obs: 98.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 51.14 Å2 / CC1/2: 0.96 / Net I/σ(I): 6.88 |
Reflection shell | Resolution: 2.21→2.34 Å / Num. unique obs: 6300 / CC1/2: 0.69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FLF Resolution: 2.21→47.38 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.271 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.19
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Displacement parameters | Biso max: 148.74 Å2 / Biso mean: 52.91 Å2 / Biso min: 28.56 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.21→47.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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