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Yorodumi- PDB-6no2: ADP bound to K114bD mutant ATP-grasp fold of Blastocystis hominis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6no2 | ||||||
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Title | ADP bound to K114bD mutant ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase | ||||||
Components | Succinate--CoA ligase [ADP-forming] subunit beta | ||||||
Keywords | LIGASE / Complex / Mutant | ||||||
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: 2.159 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 | 6no2.cif.gz | 266.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6no2.ent.gz | 227.7 KB | Display | PDB format |
PDBx/mmJSON format | 6no2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6no2_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6no2_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6no2_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 6no2_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/6no2 ftp://data.pdbj.org/pub/pdb/validation_reports/no/6no2 | HTTPS FTP |
-Related structure data
Related structure data | 6no0C 6no1C 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 27596.965 Da / Num. of mol.: 2 / Fragment: UNP residues 16-253 / Mutation: K114D 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 | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 2.53 Å3/Da / Density % sol: 51.38 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 12% w/v PEG3350, 100 mM MES, pH 5.3, 225 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: May 19, 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: 2.159→54.56 Å / Num. obs: 29604 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 34.53 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.3 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 2.159→54.544 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 27.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 217.4 Å2 / Biso mean: 58.8993 Å2 / Biso min: 19.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.159→54.544 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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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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