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Yorodumi- PDB-8gmi: Citrate Synthase (CitA) in Mycobacterium tuberculosis modified by... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gmi | ||||||
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Title | Citrate Synthase (CitA) in Mycobacterium tuberculosis modified by Ebselen at C143 residue | ||||||
Components | citrate synthase | ||||||
Keywords | CYTOSOLIC PROTEIN / Citrate Synthesis / TCA cycle / cysteine modified by Ebselen | ||||||
Function / homology | Function and homology information citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Pathirage, R. / Ronning, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Rsc Med Chem / Year: 2023 Title: Mycobacterium tuberculosis CitA activity is modulated by cysteine oxidation and pyruvate binding. Authors: Pathirage, R. / Favrot, L. / Petit, C. / Yamsek, M. / Singh, S. / Mallareddy, J.R. / Rana, S. / Natarajan, A. / Ronning, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gmi.cif.gz | 546.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gmi.ent.gz | 452.6 KB | Display | PDB format |
PDBx/mmJSON format | 8gmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/8gmi ftp://data.pdbj.org/pub/pdb/validation_reports/gm/8gmi | HTTPS FTP |
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-Related structure data
Related structure data | 8gi7C 8giwC 8glbC 8gllC 8gm9C 8gmfC 8gmkC 8s97C 8s9dC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 41019.605 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: citA, SAMEA2683035_02214 / Production host: Escherichia coli (E. coli) References: UniProt: A0A045JB88, citrate synthase (unknown stereospecificity) #2: Chemical | ChemComp-9JT / #3: Chemical | ChemComp-FLC / #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: 3.44 Å3/Da / Density % sol: 64.25 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.2 M Lithium sulfate, 0.1 M HEPES pH 7.5 and 25 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→63.06 Å / Num. obs: 124596 / % possible obs: 99.91 % / Redundancy: 7.6 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.08717 / Rrim(I) all: 0.2406 / Net I/σ(I): 6.79 |
Reflection shell | Resolution: 2.7→2.797 Å / Num. unique obs: 12322 / CC1/2: 0.476 / CC star: 0.803 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→63.06 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→63.06 Å
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Refine LS restraints |
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LS refinement shell |
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