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Yorodumi- PDB-6abv: Crystal structure of citrate synthase (Msed_0281) from Metallosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6abv | ||||||
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Title | Crystal structure of citrate synthase (Msed_0281) from Metallosphaera sedula | ||||||
Components | Citrate synthase | ||||||
Keywords | TRANSFERASE / Citrate synthase / Metallosphaera sedula | ||||||
Function / homology | Function and homology information citrate synthase (unknown stereospecificity) / citrate synthase activity / tricarboxylic acid cycle / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Metallosphaera sedula (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Lee, S.-H. / Kim, K.-J. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Crystal structure and biochemical properties of msed_0281, the citrate synthase from Metallosphaera sedula. Authors: Lee, S.H. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6abv.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6abv.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 6abv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/6abv ftp://data.pdbj.org/pub/pdb/validation_reports/ab/6abv | HTTPS FTP |
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-Related structure data
Related structure data | 6abwC 1gvmS 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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Unit cell |
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-Components
#1: Protein | Mass: 43629.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Metallosphaera sedula (strain ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2) (archaea) Strain: ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2 / Gene: Msed_0281 / Production host: Escherichia coli (E. coli) References: UniProt: A4YDF6, citrate synthase (unknown stereospecificity) | ||
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#2: Chemical | #3: 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: 2.16 Å3/Da / Density % sol: 42.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 35% v/v (+/-)-2-Methyl-2,4- pentandiol (MPD), 0.1 M Bis-Tris, pH 5.0, and 0.2 M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→65.12 Å / Num. obs: 34475 / % possible obs: 98 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 45.7 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.308 / Num. unique obs: 1703 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GVM Resolution: 1.8→65.11 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.514 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.127 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.44 Å2 / Biso mean: 27.804 Å2 / Biso min: 10.16 Å2
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Refinement step | Cycle: final / Resolution: 1.8→65.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.803→1.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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