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Yorodumi- PDB-5dql: Crystal Structure of 2-vinyl glyoxylate modified isocitrate lyase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dql | ||||||
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Title | Crystal Structure of 2-vinyl glyoxylate modified isocitrate lyase from Mycobacterium tuberculosis | ||||||
Components | Isocitrate lyase 1 | ||||||
Keywords | LYASE/LYASE INHIBITOR / LYASE-LYASE INHIBITOR complex | ||||||
Function / homology | Function and homology information methylisocitrate lyase / glyoxysome / methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / isocitrate metabolic process / response to host immune response / zymogen binding / glyoxylate cycle / tricarboxylic acid cycle ...methylisocitrate lyase / glyoxysome / 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: 1.782 Å | ||||||
Authors | Huang, H.-L. / Meek, T.D. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Mechanism-based inactivator of isocitrate lyases 1 and 2 from Mycobacterium tuberculosis. Authors: Pham, T.V. / Murkin, A.S. / Moynihan, M.M. / Harris, L. / Tyler, P.C. / Shetty, N. / Sacchettini, J.C. / Huang, H.L. / 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 | 5dql.cif.gz | 360.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dql.ent.gz | 291.5 KB | Display | PDB format |
PDBx/mmJSON format | 5dql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dql_validation.pdf.gz | 477.5 KB | Display | wwPDB validaton report |
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Full document | 5dql_full_validation.pdf.gz | 498.3 KB | Display | |
Data in XML | 5dql_validation.xml.gz | 72.2 KB | Display | |
Data in CIF | 5dql_validation.cif.gz | 104.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/5dql ftp://data.pdbj.org/pub/pdb/validation_reports/dq/5dql | HTTPS FTP |
-Related structure data
Related structure data | 1f8mS 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
#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 35801 / TMC 107 / Erdman) (bacteria) Strain: ATCC 35801 / TMC 107 / Erdman / Gene: icl1, ERDMAN_0512, Q643_00485 / Plasmid: pET30(b) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: H8EVV4, UniProt: P9WKK7*PLUS, isocitrate lyase, methylisocitrate lyase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-VGX / #4: Water | ChemComp-HOH / | |
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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: 2.16 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 4000, Sodium acetate, Tris-HCl / PH range: 7.5-8.5 / Temp details: Varies between 289-291K |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid N2 cryo stream |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→42.31 Å / Num. obs: 155652 / % possible obs: 99.6 % / Redundancy: 7.7 % / Rsym value: 0.0408 / Net I/σ(I): 14.01 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 0.45 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F8M Resolution: 1.782→34.274 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.71 / 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: 1.782→34.274 Å
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Refine LS restraints |
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LS refinement shell |
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