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Yorodumi- PDB-6fm3: Deoxyguanylosuccinate synthase (DgsS) structure with ADP at 1.9 A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fm3 | ||||||
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Title | Deoxyguanylosuccinate synthase (DgsS) structure with ADP at 1.9 Angstrom resolution | ||||||
Components | Adenylosuccinate synthetase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / 2 / 6-diaminopurine / phage phiVC8 / Synthetase | ||||||
Function / homology | Function and homology information 2-amino-2'-deoxyadenylo-succinate synthase / adenylosuccinate synthase activity / IMP metabolic process / 'de novo' AMP biosynthetic process / purine nucleotide biosynthetic process / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio phage phiVC8 (virus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.95 Å | ||||||
Authors | Sleiman, D. / Loc'h, J. / Haouz, A. / Kaminski, P.A. | ||||||
Citation | Journal: To Be Published Title: Deoxyguanylosuccinate synthase (DgsS) quaternary structure with ATP0, dGMP, Magnesium at 2.3 Angstrom resolution Authors: Sleiman, D. / Loc'h, J. / Haouz, A. / 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 | 6fm3.cif.gz | 142.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fm3.ent.gz | 108.5 KB | Display | PDB format |
PDBx/mmJSON format | 6fm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fm3_validation.pdf.gz | 737.7 KB | Display | wwPDB validaton report |
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Full document | 6fm3_full_validation.pdf.gz | 740.8 KB | Display | |
Data in XML | 6fm3_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 6fm3_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/6fm3 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/6fm3 | HTTPS FTP |
-Related structure data
Related structure data | |
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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 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: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-CL / |
#4: 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: 2.25 Å3/Da / Density % sol: 45.27 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / Details: 2M NaCl 12%w/v PEG 6K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.32 Å / Num. obs: 24769 / % possible obs: 93.7 % / Redundancy: 5.59 % / Biso Wilson estimate: 41.98 Å2 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.3→2.44 Å |
-Processing
Software |
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Refinement | Resolution: 1.95→48.32 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.216 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.166
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Displacement parameters | Biso mean: 36.62 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.95→48.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.04 Å / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: -11.3624 Å / Origin y: -11.4532 Å / Origin z: 21.3026 Å
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Refinement TLS group | Selection details: { A|* } |