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Yorodumi- PDB-6edz: Crystal structure of Mycobacterium tuberculosis ICL2 in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6edz | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis ICL2 in complex with acetyl-CoA, form I | ||||||
Components | Isocitrate lyase 2 | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information isocitrate lyase / isocitrate lyase activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å | ||||||
Authors | Bashiri, G. / Bhusal, R. / Leung, I. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Acetyl-CoA-mediated activation of Mycobacterium tuberculosis isocitrate lyase 2. Authors: Bhusal, R.P. / Jiao, W. / Kwai, B.X.C. / Reynisson, J. / Collins, A.J. / Sperry, J. / Bashiri, G. / Leung, I.K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6edz.cif.gz | 564 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6edz.ent.gz | 477.7 KB | Display | PDB format |
PDBx/mmJSON format | 6edz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6edz_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6edz_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6edz_validation.xml.gz | 97.2 KB | Display | |
Data in CIF | 6edz_validation.cif.gz | 132.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/6edz ftp://data.pdbj.org/pub/pdb/validation_reports/ed/6edz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 87615.977 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria) Strain: CDC 1551 / Oshkosh / Gene: icl2, aceA-2, MT1966 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VJU4, isocitrate lyase #2: Chemical | ChemComp-ACO / #3: 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: 2.74 Å3/Da / Density % sol: 55.07 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 9% w/v PEG 4K, 18% v/v glycerol, 0.02 M amino acids, 0.1 M MES/imidazole pH 6.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→106.6 Å / Num. obs: 106792 / % possible obs: 100 % / Redundancy: 7 % / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.67→2.72 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→49.34 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.924 / SU B: 16.515 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R: 1.045 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.248 Å2
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Refinement step | Cycle: 1 / Resolution: 2.67→49.34 Å
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Refine LS restraints |
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