[English] 日本語
Yorodumi- PDB-3ahf: Phosphoketolase from Bifidobacterium Breve complexed with inorgan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ahf | ||||||
---|---|---|---|---|---|---|---|
Title | Phosphoketolase from Bifidobacterium Breve complexed with inorganic phosphate | ||||||
Components | Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase | ||||||
Keywords | LYASE / THIAMINE DIPHOSPHATE-DEPENDENT ENZYME / ALPHA-BETA FOLD / HOMODIMER / INORGANIC PHOSPHATE | ||||||
Function / homology | Function and homology information Lyases; Carbon-carbon lyases; Aldehyde-lyases / aldehyde-lyase activity / carbohydrate metabolic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Bifidobacterium breve (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Suzuki, R. / Katayama, T. / Kim, B.-J. / Wakagi, T. / Shoun, H. / Ashida, H. / Yamamoto, K. / Fushinobu, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Crystal Structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism Authors: Suzuki, R. / Katayama, T. / Kim, B.-J. / Wakagi, T. / Shoun, H. / Ashida, H. / Yamamoto, K. / Fushinobu, S. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Overexpression, crystallization and preliminary X-ray analysis of xylulose-5-phosphate/fructose-6-phosphate phosphoketolase from Bifidobacterium breve Authors: Suzuki, R. / Kim, B.-J. / Shibata, T. / Iwamoto, Y. / Katayama, T. / Ashida, H. / Wakagi, T. / Shoun, H. / Fushinobu, S. / Yamamoto, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ahf.cif.gz | 188.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ahf.ent.gz | 144.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ahf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/3ahf ftp://data.pdbj.org/pub/pdb/validation_reports/ah/3ahf | HTTPS FTP |
---|
-Related structure data
Related structure data | 3ahcSC 3ahdC 3aheC 3ahgC 3ahhC 3ahiC 3ahjC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 94962.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium breve (bacteria) / Strain: 203 / Gene: xfp / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3)-RIL References: UniProt: D6PAH1, fructose-6-phosphate phosphoketolase |
---|
-Non-polymers , 5 types, 524 molecules
#2: Chemical | ChemComp-TPP / | ||
---|---|---|---|
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-PO4 / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.07 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 24%(v/v) PEG 6000, 0.1M BICINE buffer, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 30, 2008 / Details: mirrors |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 55669 / Num. obs: 55630 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 4.7 / Num. unique all: 5490 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AHC Resolution: 2.3→40.88 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.556 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.516 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→40.88 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.299→2.359 Å / Total num. of bins used: 20
|