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Yorodumi- PDB-3igx: 1.85 Angstrom Resolution Crystal Structure of Transaldolase B (ta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3igx | ||||||
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Title | 1.85 Angstrom Resolution Crystal Structure of Transaldolase B (talA) from Francisella tularensis. | ||||||
Components | Transaldolase | ||||||
Keywords | TRANSFERASE / Transaldolase B / talA / idp02095 / Pentose shunt / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information transaldolase / transaldolase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Francisella tularensis subsp. tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å | ||||||
Authors | Minasov, G. / Wawrzak, Z. / Skarina, T. / Gordon, E. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: 1.85 Angstrom Resolution Crystal Structure of Transaldolase B (talA) from Francisella tularensis. Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Gordon, E. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3igx.cif.gz | 156.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3igx.ent.gz | 129.6 KB | Display | PDB format |
PDBx/mmJSON format | 3igx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/3igx ftp://data.pdbj.org/pub/pdb/validation_reports/ig/3igx | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36285.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria) Strain: tularensis SCHU S4 / Gene: FTT1093c, FTT_1093c, talA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / 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: 2.43 Å3/Da / Density % sol: 49.43 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein solution: 0.3M NaCl, 10mM HEPES (pH 7.5). Screen solution: 50mM Potassium Dhydrogen phosphate, 20% PEG 8000; Cryo solution: 5% Glycerol, 5% Sucrose, 5% Ethelene Glycol in screen ...Details: Protein solution: 0.3M NaCl, 10mM HEPES (pH 7.5). Screen solution: 50mM Potassium Dhydrogen phosphate, 20% PEG 8000; Cryo solution: 5% Glycerol, 5% Sucrose, 5% Ethelene Glycol in screen solution, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97921 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 24, 2009 / Details: mirrors |
Radiation | Monochromator: Si {1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. all: 62081 / Num. obs: 62081 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 3 / Num. unique all: 2873 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.85→29.41 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.151 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Individual Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.114 / 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: 12.646 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→29.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 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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