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Yorodumi- PDB-6no1: ADP bound to K46bE mutant ATP-grasp fold of Blastocystis hominis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6no1 | ||||||
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Title | ADP bound to K46bE mutant ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase | ||||||
Components | Succinate--CoA ligase [ADP-forming] subunit beta | ||||||
Keywords | LIGASE / Mutant / Complex | ||||||
Function / homology | Function and homology information hydrogenosome / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / magnesium ion binding / mitochondrion / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Blastocystis sp. subtype 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.44 Å | ||||||
Authors | Huang, J. / Fraser, M.E. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: ATP-specificity of succinyl-CoA synthetase from Blastocystis hominis. Authors: Huang, J. / Nguyen, V.H. / Hamblin, K.A. / Maytum, R. / van der Giezen, M. / Fraser, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6no1.cif.gz | 256.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6no1.ent.gz | 221.3 KB | Display | PDB format |
PDBx/mmJSON format | 6no1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6no1_validation.pdf.gz | 756.7 KB | Display | wwPDB validaton report |
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Full document | 6no1_full_validation.pdf.gz | 760.9 KB | Display | |
Data in XML | 6no1_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 6no1_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/6no1 ftp://data.pdbj.org/pub/pdb/validation_reports/no/6no1 | HTTPS FTP |
-Related structure data
Related structure data | 6no0C 6no2C 6no3C 6no4C 6no5C 6no6C 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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Unit cell |
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-Components
#1: Protein | Mass: 27610.992 Da / Num. of mol.: 2 / Fragment: UNP residues 16-253 / Mutation: K46E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Blastocystis sp. subtype 1 (strain ATCC 50177 / NandII) (eukaryote) Strain: ATCC 50177 / NandII / Gene: SCSb / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B3FHP0, succinate-CoA ligase (ADP-forming) #2: Chemical | ChemComp-ADP / | #3: Chemical | #4: 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: 2.37 Å3/Da / Density % sol: 48.03 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 15% w/v PEG3350, 100 mM MES, pH 5.9, 125 mM ammonium tartrate, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 4, 2018 | |||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.44→80.12 Å / Num. obs: 20700 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 8 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 2.44→69.235 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 38.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 273.11 Å2 / Biso mean: 101.9796 Å2 / Biso min: 31.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.44→69.235 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %
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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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