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Yorodumi- PDB-8gmk: Pyruvate bound structure of Citrate Synthase (CitA) in Mycobacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gmk | |||||||||
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Title | Pyruvate bound structure of Citrate Synthase (CitA) in Mycobacterium Tuberculosis | |||||||||
Components | citrate synthase | |||||||||
Keywords | CYTOSOLIC PROTEIN / Citrate Synthesis / TCA cycle / pyruvate | |||||||||
Function / homology | Function and homology information citrate synthase (unknown stereospecificity) / citrate synthase activity / tricarboxylic acid cycle Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | |||||||||
Authors | Pathirage, R. / Ronning, D. / Yamsek, M. | |||||||||
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 | 8gmk.cif.gz | 163.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gmk.ent.gz | 126.4 KB | Display | PDB format |
PDBx/mmJSON format | 8gmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/8gmk ftp://data.pdbj.org/pub/pdb/validation_reports/gm/8gmk | HTTPS FTP |
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-Related structure data
Related structure data | 8gi7C 8giwC 8glbC 8gllC 8gm9C 8gmfC 8gmiC 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41019.605 Da / Num. of mol.: 2 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) |
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-Non-polymers , 5 types, 491 molecules
#2: Chemical | #3: Chemical | ChemComp-PGE / | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PEG / #6: Water | ChemComp-HOH / | |
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-Details
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: 2.46 Å3/Da / Density % sol: 50.06 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris pH 8.5, 0.5 M sodium chloride and 19 % w/v polyethylene glycol 3350 in the presence of 5.6 micromolar detergent, CYMAL-6 |
-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: Jul 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→41.34 Å / Num. obs: 74189 / % possible obs: 99.87 % / Redundancy: 9.7 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.05 / Rrim(I) all: 0.156 / Χ2: 1.479 / Net I/σ(I): 13.12 |
Reflection shell | Resolution: 1.81→1.875 Å / Redundancy: 8.8 % / Rmerge(I) obs: 2.453 / Num. unique obs: 7262 / CC1/2: 0.415 / CC star: 0.766 / Rpim(I) all: 0.863 / Rrim(I) all: 2.603 / Χ2: 0.639 / % possible all: 99.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→41.34 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.16 / 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: 1.81→41.34 Å
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Refine LS restraints |
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LS refinement shell |
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