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Yorodumi- PDB-3mbd: Crystal structure of fructose bisphosphate aldolase from Encephal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mbd | ||||||
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Title | Crystal structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi, bound to phosphate | ||||||
Components | Fructose-bisphosphate aldolase | ||||||
Keywords | LYASE / ALDOLASE / Glycolysis / Schiff base / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 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 | 3mbd.cif.gz | 150 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mbd.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mbd_validation.pdf.gz | 429.9 KB | Display | wwPDB validaton report |
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Full document | 3mbd_full_validation.pdf.gz | 430.6 KB | Display | |
Data in XML | 3mbd_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 3mbd_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/3mbd ftp://data.pdbj.org/pub/pdb/validation_reports/mb/3mbd | HTTPS FTP |
-Related structure data
Related structure data | 3mbfC 1qo5S 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
#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: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-CL / |
#4: 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: 3.41 Å3/Da / Density % sol: 63.95 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 90% PACT SCREEN CONDITION F10, 10% ADDITIVE SCREEN G12: 90MM BIS-TRIS PROPANE PH 6.5, 18% PEG 3350, 18 MM NAKHPO4, 10 MM UREA, 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: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 11, 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→36.8 Å / Num. all: 35792 / Num. obs: 35720 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.83 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.6 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QO5 Resolution: 2→35.34 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.361 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.113 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.39 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 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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