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- PDB-6abx: Crystal structure of citrate synthase (Msed_1522) from Metallosph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6abx | ||||||
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Title | Crystal structure of citrate synthase (Msed_1522) from Metallosphaera sedula in complex with citrate | ||||||
![]() | Citrate synthase | ||||||
![]() | TRANSFERASE / Citrate synthase / Metallosphaera sedula | ||||||
Function / homology | ![]() citrate synthase activity / citrate synthase (unknown stereospecificity) / tricarboxylic acid cycle / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, S.-H. / Son, H.-F. / Kim, K.-J. | ||||||
![]() | ![]() Title: Structural insights into the inhibition properties of archaeon citrate synthase from Metallosphaera sedula. Authors: Lee, S.H. / Son, H.F. / Kim, K.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.9 KB | Display | ![]() |
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PDB format | ![]() | 134.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.6 KB | Display | ![]() |
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Full document | ![]() | 474.2 KB | Display | |
Data in XML | ![]() | 34.4 KB | Display | |
Data in CIF | ![]() | 50.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6abyC ![]() 1vgpS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43230.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2 / Gene: Msed_1522 / Production host: ![]() ![]() References: UniProt: A4YGX6, citrate synthase (unknown stereospecificity) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.39 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 800mM sodium phosphate monobasic/1200mM potassium phosphate dibasic, 0.1 M sodium acetate/acetic acid pH 4.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 15, 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: 1.7→72.84 Å / Num. obs: 79198 / % possible obs: 97.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.263 / Num. unique obs: 1703 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VGP Resolution: 1.7→29.15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.847 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.093 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: 82.2 Å2 / Biso mean: 21.068 Å2 / Biso min: 3.43 Å2
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Refinement step | Cycle: final / Resolution: 1.7→29.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.698→1.742 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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