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- PDB-3ahg: H64A mutant of Phosphoketolase from Bifidobacterium Breve complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ahg | ||||||
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Title | H64A mutant of Phosphoketolase from Bifidobacterium Breve complexed with a tricyclic ring form of thiamine diphosphate | ||||||
![]() | Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase | ||||||
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Function / homology | ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suzuki, R. / Katayama, T. / Kim, B.-J. / Wakagi, T. / Shoun, H. / Ashida, H. / Yamamoto, K. / Fushinobu, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.9 KB | Display | ![]() |
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PDB format | ![]() | 151.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ahcSC ![]() 3ahdC ![]() 3aheC ![]() 3ahfC ![]() 3ahhC ![]() 3ahiC ![]() 3ahjC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 94895.820 Da / Num. of mol.: 1 / Mutation: H64A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: D6PAH1, ![]() |
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-Non-polymers , 5 types, 833 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/HTD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HTD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / | ||
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#3: Chemical | ChemComp-HTD / | ||
#4: Chemical | ChemComp-NA / | ||
#5: Chemical | ChemComp-EDO / ![]() #6: Water | ChemComp-HOH / | ![]() |
-Details
Nonpolymer details | THE LIGANDS STANDS FOR DIHYDROTHI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.59 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2009 / 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![]() |
Reflection | Resolution: 1.9→50 Å / Num. all: 99057 / Num. obs: 98341 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 57.6 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 8.8 / Num. unique all: 4862 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3AHC Resolution: 1.9→33.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.465 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.112 / 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: 27.474 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→33.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
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