[English] 日本語
Yorodumi- PDB-3bv4: Crystal structure of a rabbit muscle fructose-1,6-bisphosphate al... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bv4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a rabbit muscle fructose-1,6-bisphosphate aldolase A dimer variant | ||||||
Components | Fructose-bisphosphate aldolase A | ||||||
Keywords | LYASE / Acetylation / Glycolysis / Phosphoprotein / Schiff base | ||||||
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 / glycolytic process / protein homotetramerization / positive regulation of cell migration Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Sherawat, M. / Tolan, D.R. / Allen, K.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structure of a rabbit muscle fructose-1,6-bisphosphate aldolase A dimer variant. Authors: Sherawat, M. / Tolan, D.R. / Allen, K.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3bv4.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3bv4.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 3bv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/3bv4 ftp://data.pdbj.org/pub/pdb/validation_reports/bv/3bv4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1aldS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 37051.391 Da / Num. of mol.: 1 / Mutation: D128V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ALDOA / Plasmid: pPB1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P00883, fructose-bisphosphate aldolase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-13P / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.53 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 0.2 M ammonium sulfate, 25% PEG 2K monomethyl ether, 100 mM sodium acetate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2006 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→100 Å / Num. all: 41975 / Num. obs: 41975 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Χ2: 1.561 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 7.3 / Num. unique all: 4177 / Rsym value: 7.3 / Χ2: 1.668 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: pdb entry 1ALD Resolution: 1.7→19.51 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1463854.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.636 Å2 / ksol: 0.378 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.1 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.51 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|