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Yorodumi- PDB-5gk5: Apo structure of fructose 1,6-bisphosphate aldolase from Escheric... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gk5 | ||||||
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Title | Apo structure of fructose 1,6-bisphosphate aldolase from Escherichia coli at 1.9 angstrom resolution | ||||||
Components | Fructose-bisphosphate aldolase class 2 | ||||||
Keywords | LYASE / FBA apo3 | ||||||
Function / homology | Function and homology information fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / gluconeogenesis / glycolytic process / protein homodimerization activity / zinc ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Tran, T.H. / Huynh, K.H. / Ho, T.H. / Kang, L.W. | ||||||
Citation | Journal: To Be Published Title: Apo structure of fructose 1,6-bisphosphate aldolase from Escherichia coli at 1.9 angstrom resolution Authors: Tran, T.H. / Huynh, K.H. / Ho, T.H. / Kang, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gk5.cif.gz | 533.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gk5.ent.gz | 436.6 KB | Display | PDB format |
PDBx/mmJSON format | 5gk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gk5_validation.pdf.gz | 515.6 KB | Display | wwPDB validaton report |
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Full document | 5gk5_full_validation.pdf.gz | 537.1 KB | Display | |
Data in XML | 5gk5_validation.xml.gz | 100.5 KB | Display | |
Data in CIF | 5gk5_validation.cif.gz | 139 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/5gk5 ftp://data.pdbj.org/pub/pdb/validation_reports/gk/5gk5 | HTTPS FTP |
-Related structure data
Related structure data | 1dosS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39191.152 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: fbaA, fba, fda, b2925, JW2892 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AB71, fructose-bisphosphate aldolase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-PEG / #5: 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: 2.32 Å3/Da / Density % sol: 47.04 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M ammonium acetate, 1mM Docosahexaenoic acid , 0.1M Tris pH 7.0, and 15% PEG 4000 PH range: 5.6-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2014 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 220041 / % possible obs: 95.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.3 / % possible all: 94.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DOS Resolution: 1.9→22.055 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.97 / Phase error: 21.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→22.055 Å
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Refine LS restraints |
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LS refinement shell |
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