+Open data
-Basic information
Entry | Database: PDB / ID: 3ahj | ||||||
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Title | H553A mutant of Phosphoketolase from Bifidobacterium Breve | ||||||
Components | Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase | ||||||
Keywords | LYASE / THIAMINE DIPHOSPHATE-DEPENDENT ENZYME / ALPHA-BETA FOLD / HOMODIMER | ||||||
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 | 3ahj.cif.gz | 189.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ahj.ent.gz | 145.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ahj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/3ahj ftp://data.pdbj.org/pub/pdb/validation_reports/ah/3ahj | HTTPS FTP |
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-Related structure data
Related structure data | 3ahcSC 3ahdC 3aheC 3ahfC 3ahgC 3ahhC 3ahiC 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
#1: Protein | Mass: 94895.820 Da / Num. of mol.: 1 / Mutation: H553A 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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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | ChemComp-TPP / | ||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.7 % |
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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: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 2, 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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 74103 / Num. obs: 73937 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 42.1 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 6.9 / Num. unique all: 3652 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AHC Resolution: 2.1→38.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.1 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.129 / 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: 29.644 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→38.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.098→2.152 Å / Total num. of bins used: 20
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