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Yorodumi- PDB-6cj4: CRYSTAL STRUCTURE OF PROTEIN CITE FROM MYCOBACTERIUM TUBERCULOSIS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cj4 | ||||||
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Title | CRYSTAL STRUCTURE OF PROTEIN CITE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM AND ACETOACETATE | ||||||
Components | Citrate lyase subunit beta-like proteinATP citrate synthase | ||||||
Keywords | LYASE / PROTEIN CITE / MYCOBACTERIUM TUBERCULOSIS / ACETOACETATE / TIM-BARREL | ||||||
Function / homology | Function and homology information Lyases; Carbon-carbon lyases / oxaloacetate metabolic process / lyase activity / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Wang, H. / Bonanno, J.B. / Carvalho, L. / Almo, S.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: An essential bifunctional enzyme inMycobacterium tuberculosisfor itaconate dissimilation and leucine catabolism. Authors: Wang, H. / Fedorov, A.A. / Fedorov, E.V. / Hunt, D.M. / Rodgers, A. / Douglas, H.L. / Garza-Garcia, A. / Bonanno, J.B. / Almo, S.C. / de Carvalho, L.P.S. #1: Journal: Biorxiv / Year: 2018 Title: Discovery of a novel stereospecific beta-hydroxyacyl-CoA lyase/thioesterase shared by three metabolic pathways in Mycobacterium tuberculosis Authors: Wang, H. / Fedorov, A.A. / Fedorov, E.V. / Hunt, D.M. / Rodgers, A. / Garza-Garcia, A. / Bonanno, J.B. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cj4.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cj4.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 6cj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/6cj4 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/6cj4 | HTTPS FTP |
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-Related structure data
Related structure data | 6aq4C 6arbC 6as5C 6chuSC 6cj3C 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: 29951.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: citE, Rv2498c / Production host: Escherichia coli (E. coli) References: UniProt: P9WPE1, UniProt: P9WPE0*PLUS, Lyases; Carbon-carbon lyases |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-AAE / |
#5: 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: 2.99 Å3/Da / Density % sol: 58.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: magnesium chloride, acetoacetate, sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→25 Å / Num. obs: 72324 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.73→1.7584 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CHU Resolution: 1.73→25 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.11 / Phase error: 20.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→25 Å
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Refine LS restraints |
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LS refinement shell |
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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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