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Yorodumi- PDB-3mbf: Crystal structure of fructose bisphosphate aldolase from Encephal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mbf | ||||||
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Title | Crystal structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi, bound to fructose 1,6-bisphosphate | ||||||
Components | Fructose-bisphosphate aldolase | ||||||
Keywords | LYASE / Seattle Structural Genomics Center for Infectious Disease / (SSGCID) / ALDOLASE / Glycolysis / Schiff base | ||||||
Function / homology | Function and homology information fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / glycolytic process / cytosol Similarity search - Function | ||||||
Biological species | Encephalitozoon cuniculi (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.37 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi. Authors: Gardberg, A. / Sankaran, B. / Davies, D. / Bhandari, J. / Staker, B. / Stewart, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mbf.cif.gz | 147.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mbf.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 3mbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/3mbf ftp://data.pdbj.org/pub/pdb/validation_reports/mb/3mbf | HTTPS FTP |
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-Related structure data
Related structure data | 3mbdC 3mdbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-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: 38263.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU01_0240 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8SSM8, fructose-bisphosphate aldolase |
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#2: Sugar | ChemComp-2FP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.91 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: BASED ON PACT SCREEN CONDITION F10 WITHOUT NAKHPO4: 100MM BIS-TRIS PROPANE PH 6.5, 20% PEG 3350, 20 MM FRUCTOSE 1,6-BISPHOSPHATE, PROTEIN AT 24.7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9774 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 19, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→28.03 Å / Num. all: 21111 / Num. obs: 21046 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 37.35 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.35 |
Reflection shell | Resolution: 2.37→2.43 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1557 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3MDB Resolution: 2.37→28.03 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.8 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.37→28.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.37→2.43 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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