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Yorodumi- PDB-3tk7: 2.0 Angstrom Resolution Crystal Structure of Transaldolase B (Tal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tk7 | ||||||
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Title | 2.0 Angstrom Resolution Crystal Structure of Transaldolase B (TalA) from Francisella tularensis in Covalent Complex with Fructose 6-Phosphate | ||||||
Components | Transaldolase | ||||||
Keywords | TRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Alpha-Beta Barrel/TIM Barrel | ||||||
Function / homology | Function and homology information transaldolase / transaldolase activity / pentose-phosphate shunt, non-oxidative branch / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Francisella tularensis subsp. tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Light, S.H. / Minasov, G. / Halavaty, A.S. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Adherence to Burgi-Dunitz stereochemical principles requires significant structural rearrangements in Schiff-base formation: insights from transaldolase complexes. Authors: Light, S.H. / Minasov, G. / Duban, M.E. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tk7.cif.gz | 281.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tk7.ent.gz | 227.6 KB | Display | PDB format |
PDBx/mmJSON format | 3tk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tk7_validation.pdf.gz | 951.5 KB | Display | wwPDB validaton report |
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Full document | 3tk7_full_validation.pdf.gz | 957.3 KB | Display | |
Data in XML | 3tk7_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 3tk7_validation.cif.gz | 48 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/3tk7 ftp://data.pdbj.org/pub/pdb/validation_reports/tk/3tk7 | HTTPS FTP |
-Related structure data
Related structure data | 3te9C 3tkfC 3tnoC 4e0cC 3igxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38476.074 Da / Num. of mol.: 2 / Fragment: Transaldolase B (TalA) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria) Strain: SCHU S4 / Gene: FTT_1093c, talA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q5NFX0, transaldolase #2: Chemical | #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: 2.23 Å3/Da / Density % sol: 44.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein: 11.2 mg/ml, 0.5 M sodium chloride, 0.01 M Tris-HCl (pH 8.3), 0.005 M Fructose 6-phosphate Screen: Classics II D6 (Qiagen), 0.1 M Bis-tris, 25% (w/v) PEG 3350, VAPOR DIFFUSION, ...Details: Protein: 11.2 mg/ml, 0.5 M sodium chloride, 0.01 M Tris-HCl (pH 8.3), 0.005 M Fructose 6-phosphate Screen: Classics II D6 (Qiagen), 0.1 M Bis-tris, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 4, 2011 / Details: Beryllium lenses |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 47501 / Num. obs: 47501 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2331 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IGX Resolution: 2→28.99 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.096 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R Free: 0.171 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.004 Å2
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Refinement step | Cycle: LAST / Resolution: 2→28.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.999→2.051 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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