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Yorodumi- PDB-6wsi: Intact cis-2,3-epoxysuccinic acid bound to Isocitrate Lyase-1 fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wsi | ||||||
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Title | Intact cis-2,3-epoxysuccinic acid bound to Isocitrate Lyase-1 from Mycobacterium tuberculosis | ||||||
Components | Isocitrate lyase | ||||||
Keywords | LYASE / enzyme / covalent inhibitor / substrate analog / Structural Genomics / PSI-Biology / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information isocitrate lyase / isocitrate lyase activity / carboxylic acid metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 Å | ||||||
Authors | Krieger, I.V. / Mellott, D. / Meek, T.D. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC) | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2021 Title: Covalent Inactivation of Mycobacterium tuberculosis Isocitrate Lyase by cis -2,3-Epoxy-Succinic Acid. Authors: Pham, T.V. / Mellott, D.M. / Moghadamchargari, Z. / Chen, K. / Krieger, I. / Laganowsky, A. / Sacchettini, J.C. / Meek, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wsi.cif.gz | 366 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wsi.ent.gz | 294.8 KB | Display | PDB format |
PDBx/mmJSON format | 6wsi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/6wsi ftp://data.pdbj.org/pub/pdb/validation_reports/ws/6wsi | HTTPS FTP |
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-Related structure data
Related structure data | 6vb9C 1f8iS 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 47134.391 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: aceA_1, aceA, aceA_2, icl1, DSI38_20225, E5M05_01375, ERS007661_00054, ERS007670_00334, ERS007681_01797, ERS007688_01303, ERS007703_00218, ERS007720_01262, ERS007722_00697, ERS007741_02575, ...Gene: aceA_1, aceA, aceA_2, icl1, DSI38_20225, E5M05_01375, ERS007661_00054, ERS007670_00334, ERS007681_01797, ERS007688_01303, ERS007703_00218, ERS007720_01262, ERS007722_00697, ERS007741_02575, ERS013471_01927, ERS023446_00716, ERS024276_00897, ERS027646_00855, ERS027659_01610, ERS027661_00891, ERS075361_01798, ERS094182_00218, F6W99_03123, FRD82_04680, SAMEA2683035_00941 Production host: Escherichia coli (E. coli) / References: UniProt: A0A045H6H0, isocitrate lyase |
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-Non-polymers , 6 types, 1210 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GLV / #4: Chemical | ChemComp-U9S / ( #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-PEG / #7: 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: 2.27 Å3/Da / Density % sol: 45.79 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris pH 8.0, 0.2 M NaAc, 25% PEG 4,000 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.749→71.048 Å / Num. obs: 172875 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.043 / Rrim(I) all: 0.107 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.75→1.8 Å / Rmerge(I) obs: 1.008 / Mean I/σ(I) obs: 1 / Num. unique obs: 12489 / CC1/2: 0.544 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F8I Resolution: 1.749→71.048 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.14 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.84 Å2 / Biso mean: 24.0292 Å2 / Biso min: 12.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.749→71.048 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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