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Yorodumi- PDB-3kof: Crystal structure of the double mutant F178Y/R181E of E.coli tran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kof | ||||||
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Title | Crystal structure of the double mutant F178Y/R181E of E.coli transaldolase B | ||||||
Components | Transaldolase BTransaldolase | ||||||
Keywords | TRANSFERASE / TRANSALDOLASE / ALDOLASE / DIRECTED EVOLUTION / CYTOPLASM / PENTOSE SHUNT | ||||||
Function / homology | Function and homology information transketolase or transaldolase activity / transaldolase / transaldolase activity / pentose-phosphate shunt, non-oxidative branch / carbohydrate metabolic process / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Schneider, S. / Gutierrez, M. / Sandalova, T. / Schneider, G. / Clapes, P. / Sprenger, G.A. / Samland, A.K. | ||||||
Citation | Journal: Chembiochem / Year: 2010 Title: Redesigning the Active Site of Transaldolase TalB from Escherichia coli: New Variants with Improved Affinity towards Nonphosphorylated Substrates. Authors: Schneider, S. / Gutierrez, M. / Sandalova, T. / Schneider, G. / Clapes, P. / Sprenger, G.A. / Samland, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kof.cif.gz | 267.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kof.ent.gz | 216.9 KB | Display | PDB format |
PDBx/mmJSON format | 3kof.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/3kof ftp://data.pdbj.org/pub/pdb/validation_reports/ko/3kof | HTTPS FTP |
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-Related structure data
Related structure data | 3cwnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 37448.461 Da / Num. of mol.: 2 / Mutation: F178Y, R181E, A247T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: W3110 / K12 / DSM 5911 / Gene: talB, yaaK, b0008, JW0007 / Plasmid: pJF119EH / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLUE / References: UniProt: P0A870, transaldolase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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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: 2.5 Å3/Da / Density % sol: 50.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M Ammonium sulfate, 18% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 59317 / Num. obs: 59317 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.55 % / Biso Wilson estimate: 19.6 Å2 / Rsym value: 0.101 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 8047 / Rsym value: 0.525 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3CWN Resolution: 1.9→48.85 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.818 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.151 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.014 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→48.85 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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