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Yorodumi- PDB-3ekl: Structural Characterization of tetrameric Mycobacterium tuberculo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ekl | ||||||
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Title | Structural Characterization of tetrameric Mycobacterium tuberculosis fructose 1,6-bisphosphate aldolase - substrate binding and catalysis mechanism of a class IIa bacterial aldolase | ||||||
Components | Fructose-bisphosphate aldolase | ||||||
Keywords | LYASE / class II fructose-1 / 6-bisphosphate aldolase / zinc enzyme / Mycobacterium tuberculosis / dihydroxyacetone / glyceraldehyde-3-phosphate / aldol condensation / Glycolysis / Metal-binding / Zinc | ||||||
Function / homology | Function and homology information fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / zymogen binding / cell wall / peptidoglycan-based cell wall / glycolytic process / zinc ion binding / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Pegan, S. / Rukseree, K. / Franzblau, S.G. / Mesecar, A.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural basis for catalysis of a tetrameric class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis Authors: Pegan, S.D. / Rukseree, K. / Franzblau, S.G. / Mesecar, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ekl.cif.gz | 94.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ekl.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ekl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/3ekl ftp://data.pdbj.org/pub/pdb/validation_reports/ek/3ekl | HTTPS FTP |
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-Related structure data
Related structure data | 3ekzC 3elfC 1b57S C: citing same article (ref.) 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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Details | The second, third, and fourth parts of the biological assembly is generated by the two fold axes: -x, -y+1, z ; x-1/2, -y+1/2, z+1/2; x, -y+1, -z. |
-Components
#1: Protein | Mass: 37276.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: fba, MT0379, MTCY13E10.25c, Rv0363c / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P67475, UniProt: P9WQA3*PLUS, fructose-bisphosphate aldolase | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Nonpolymer details | AUTHOR STATES THAT B13P IS A HYDROXY ENIOLATE INTERMEDIA | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 69.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 26% PEG 300, 0.1 NaAcetate pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→97.1 Å / Num. all: 91761 / Num. obs: 91761 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.51→1.56 Å / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology model derived from PDB ENTRY 1B57 Resolution: 1.51→97.1 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.503 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.063 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→97.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.549 Å / Total num. of bins used: 20
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