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Yorodumi- PDB-6xpp: Crystal structure of itaconate modified Mycobaterium tuberculosis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xpp | |||||||||
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Title | Crystal structure of itaconate modified Mycobaterium tuberculosis isocitrate lyase | |||||||||
Components | Isocitrate lyase | |||||||||
Keywords | LYASE / covalent modification | |||||||||
Function / homology | Function and homology information methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / isocitrate metabolic process / response to host immune response / zymogen binding / glyoxylate cycle / tricarboxylic acid cycle / cellular response to hypoxia / extracellular region ...methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / isocitrate metabolic process / response to host immune response / zymogen binding / glyoxylate cycle / tricarboxylic acid cycle / cellular response to hypoxia / extracellular region / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | |||||||||
Authors | Kwai, B.X.C. / Bashiri, G. / Leung, I.K.H. | |||||||||
Funding support | New Zealand, 2items
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Citation | Journal: Rsc Med Chem / Year: 2021 Title: Itaconate is a covalent inhibitor of the Mycobacterium tuberculosis isocitrate lyase. Authors: Kwai, B.X.C. / Collins, A.J. / Middleditch, M.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 | 6xpp.cif.gz | 382.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xpp.ent.gz | 300.1 KB | Display | PDB format |
PDBx/mmJSON format | 6xpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/6xpp ftp://data.pdbj.org/pub/pdb/validation_reports/xp/6xpp | HTTPS FTP |
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-Related structure data
Related structure data | 1f8iS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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-Components
#1: Protein | Mass: 47134.391 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: icl, Rv0467, MTV038.11 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WKK7, isocitrate lyase #2: Chemical | ChemComp-ITN / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.23 Å3/Da / Density % sol: 44.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG3350, 0.2M sodium nitrate, 0.1M bis-tris propane |
-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: 0.953733 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953733 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→49.377 Å / Num. obs: 242871 / % possible obs: 99.7 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.034 / Rrim(I) all: 0.128 / Χ2: 0.99 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 14.1 % / Rmerge(I) obs: 2.057 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 11809 / CC1/2: 0.613 / Rpim(I) all: 0.56 / Rrim(I) all: 2.133 / Χ2: 1.05 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F8I Resolution: 1.55→49.377 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.171 / WRfactor Rwork: 0.151 / SU B: 1.594 / SU ML: 0.055 / Average fsc free: 0.9317 / Average fsc work: 0.9355 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.072 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.236 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→49.377 Å
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Refine LS restraints |
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