[English] 日本語
Yorodumi- PDB-3dfp: Phosphate ions in D33N mutant fructose-1,6-bisphosphate aldolase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dfp | ||||||
---|---|---|---|---|---|---|---|
Title | Phosphate ions in D33N mutant fructose-1,6-bisphosphate aldolase from rabbit muscle | ||||||
Components | Fructose-bisphosphate aldolase A | ||||||
Keywords | LYASE / aldolase / mutant / phosphate / ion | ||||||
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: 2.05 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3dfp.cif.gz | 327 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3dfp.ent.gz | 259.4 KB | Display | PDB format |
PDBx/mmJSON format | 3dfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dfp_validation.pdf.gz | 455.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3dfp_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 3dfp_validation.xml.gz | 72.8 KB | Display | |
Data in CIF | 3dfp_validation.cif.gz | 111.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/3dfp ftp://data.pdbj.org/pub/pdb/validation_reports/df/3dfp | HTTPS FTP |
-Related structure data
Related structure data | 3dfnC 3dfoC 3dfqC 3dfsC 3dftC 1zahS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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-PO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.79 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 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: 1.9→50 Å / Num. obs: 111001 / % possible obs: 94.9 % / Redundancy: 4.8 % / Rsym value: 0.145 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 10242 / % possible all: 88.1 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ZAH Resolution: 2.05→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(I): 1
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.14 Å
|