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Yorodumi- PDB-6chu: CRYSTAL STRUCTURE OF PROTEIN CITE FROM MYCOBACTERIUM TUBERCULOSIS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6chu | ||||||
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Title | CRYSTAL STRUCTURE OF PROTEIN CITE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM AND ACETATE | ||||||
Components | Citrate lyase subunit beta-like protein | ||||||
Keywords | LYASE / PROTEIN CITE / MYCOBACTERIUM TUBERCULOSIS / ACETATE / TIM-BARREL | ||||||
Function / homology | Function and homology information Lyases; Carbon-carbon lyases / oxaloacetate metabolic process / lyase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 | 6chu.cif.gz | 111.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6chu.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 6chu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6chu_validation.pdf.gz | 447.6 KB | Display | wwPDB validaton report |
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Full document | 6chu_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 6chu_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 6chu_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/6chu ftp://data.pdbj.org/pub/pdb/validation_reports/ch/6chu | HTTPS FTP |
-Related structure data
Related structure data | 6aq4C 6arbC 6as5C 6cj3C 6cj4C 1u5hS C: citing same article (ref.) S: Starting model for refinement |
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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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-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-EDO / | #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: 2.94 Å3/Da / Density % sol: 58.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: magnesium chloride, 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: Oct 18, 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: 1.61→25 Å / Num. obs: 88184 / % possible obs: 99.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.61→1.6321 Å / Num. unique obs: 3368 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U5H Resolution: 1.61→24.767 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.87 / Phase error: 23.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→24.767 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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