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Yorodumi- PDB-3ahe: Phosphoketolase from Bifidobacterium Breve complexed with dihydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ahe | ||||||
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Title | Phosphoketolase from Bifidobacterium Breve complexed with dihydroxyethyl thiamine diphosphate | ||||||
Components | Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase | ||||||
Keywords | LYASE / THIAMINE DIPHOSPHATE-DEPENDENT ENZYME / ALPHA-BETA FOLD / HOMODIMER / DIHYDROXYETHYL THIAMINE DIPHOSPHATE | ||||||
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: 2.1 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ahe.cif.gz | 198.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ahe.ent.gz | 152.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ahe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/3ahe ftp://data.pdbj.org/pub/pdb/validation_reports/ah/3ahe | HTTPS FTP |
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-Related structure data
Related structure data | 3ahcSC 3ahdC 3ahfC 3ahgC 3ahhC 3ahiC 3ahjC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-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 |
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-Non-polymers , 6 types, 812 molecules
#2: Chemical | ChemComp-MG / | ||||
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#3: Chemical | ChemComp-THD / | ||||
#4: Chemical | ChemComp-NA / | ||||
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-2PE / | #7: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | AUTHORS STATE THAT LIGAND DENOTED AS THD IS PRESENT IN THE CRYSTAL STRUCTURE IN THE FORM OF A- ...AUTHORS STATE THAT LIGAND DENOTED AS THD IS PRESENT IN THE CRYSTAL STRUCTURE IN THE FORM OF A-CARBOANION |
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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: 3.32 Å3/Da / Density % sol: 62.91 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 25, 2010 / Details: mirrors |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 72417 / Num. obs: 72387 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.9 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 42.8 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 15 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 11 / Num. unique all: 3587 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AHC Resolution: 2.1→49.07 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.637 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 22.304 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→49.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.101→2.156 Å / Total num. of bins used: 20
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