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- PDB-1f61: CRYSTAL STRUCTURE OF ISOCITRATE LYASE FROM MYCOBACTERIUM TUBERCULOSIS -
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Open data
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Basic information
Entry | Database: PDB / ID: 1f61 | ||||||
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Title | CRYSTAL STRUCTURE OF ISOCITRATE LYASE FROM MYCOBACTERIUM TUBERCULOSIS | ||||||
![]() | ISOCITRATE LYASE | ||||||
![]() | LYASE / ALPHA-BETA BARREL / SWAPPED HELICES / APO-ENZYME / OPEN CONFORMATION / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | ![]() methylisocitrate lyase / 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 ...methylisocitrate lyase / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sharma, V. / Sharma, S. / Hoener zu Bentrup, K.H. / McKinney, J.D. / Russell, D.G. / Jacobs Jr., W.R. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC) | ||||||
![]() | ![]() Title: Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis. Authors: Sharma, V. / Sharma, S. / Hoener zu Bentrup, K. / McKinney, J.D. / Russell, D.G. / Jacobs Jr., W.R. / Sacchettini, J.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.5 KB | Display | ![]() |
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PDB format | ![]() | 147 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 369.7 KB | Display | ![]() |
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Full document | ![]() | 379.2 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 30.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 47205.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Mycobacterium tuberculosis / Strain: H37RV / Plasmid: PET30B / Production host: ![]() ![]() References: UniProt: P0A5H3, UniProt: P9WKK7*PLUS, isocitrate lyase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67.1 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: sodium citrate, HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→20 Å / Num. all: 97699 / Num. obs: 97699 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.08 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.5 | |||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 10 % / Rmerge(I) obs: 0.37 / Num. unique all: 9617 / % possible all: 100 | |||||||||||||||
Reflection | *PLUS Num. measured all: 1082279 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.37 |
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Processing
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Refinement | Resolution: 2→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 665225.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.25 Å2 / ksol: 0.387 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.244 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.211 |