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Yorodumi- PDB-3dfo: Dihydroxyacetone phosphate Schiff base and enamine intermediates ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dfo | ||||||
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Title | Dihydroxyacetone phosphate Schiff base and enamine intermediates in D33N mutant fructose-1,6-bisphosphate aldolase from rabbit muscle | ||||||
Components | Fructose-bisphosphate aldolase A | ||||||
Keywords | LYASE / aldolase / mutant / iminium / Schiff base / enamine / intermediate / covalent | ||||||
Function / homology | Function and homology information negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / M band / I band / fructose 1,6-bisphosphate metabolic process / glycolytic process / protein homotetramerization / positive regulation of cell migration / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | St-Jean, M. / Sygusch, J. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Charge stabilization and entropy reduction of central lysine residues in fructose-bisphosphate aldolase Authors: St-Jean, M. / Blonski, C. / Sygusch, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dfo.cif.gz | 326 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dfo.ent.gz | 259 KB | Display | PDB format |
PDBx/mmJSON format | 3dfo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dfo_validation.pdf.gz | 475.1 KB | Display | wwPDB validaton report |
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Full document | 3dfo_full_validation.pdf.gz | 493.5 KB | Display | |
Data in XML | 3dfo_validation.xml.gz | 73.8 KB | Display | |
Data in CIF | 3dfo_validation.cif.gz | 112 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/3dfo ftp://data.pdbj.org/pub/pdb/validation_reports/df/3dfo | HTTPS FTP |
-Related structure data
Related structure data | 3dfnC 3dfpC 3dfqC 3dfsC 3dftC 1zahS 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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-Components
#1: Protein | Mass: 39262.688 Da / Num. of mol.: 4 / Mutation: D33N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ALDOA / Plasmid: pPB14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 SI / References: UniProt: P00883, fructose-bisphosphate aldolase #2: Chemical | ChemComp-13P / #3: Water | ChemComp-HOH / | Nonpolymer details | 13P LIGAND IS COVALENTLY | |
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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: 2.3 Å3/Da / Density % sol: 46.44 % |
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Crystal grow | Temperature: 296 K / pH: 7.5 Details: sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 118077 / % possible obs: 90 % / Redundancy: 3.3 % / Rsym value: 0.083 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1 / Rsym value: 0.699 / % possible all: 50.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZAH Resolution: 1.94→43.76 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 25.24 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.94→43.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→2.03 Å
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