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Open data
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Basic information
Entry | Database: PDB / ID: 3m16 | ||||||
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Title | Structure of a Transaldolase from Oleispira antarctica | ||||||
![]() | Transaldolase | ||||||
![]() | TRANSFERASE / Oleispira antarctica / transaldolase / dimer / molecular replacement / Swiss-Model / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() transaldolase / transaldolase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Singer, A.U. / Kagan, O. / Zhang, R. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica. Authors: Kube, M. / Chernikova, T.N. / Al-Ramahi, Y. / Beloqui, A. / Lopez-Cortez, N. / Guazzaroni, M.E. / Heipieper, H.J. / Klages, S. / Kotsyurbenko, O.R. / Langer, I. / Nechitaylo, T.Y. / ...Authors: Kube, M. / Chernikova, T.N. / Al-Ramahi, Y. / Beloqui, A. / Lopez-Cortez, N. / Guazzaroni, M.E. / Heipieper, H.J. / Klages, S. / Kotsyurbenko, O.R. / Langer, I. / Nechitaylo, T.Y. / Lunsdorf, H. / Fernandez, M. / Juarez, S. / Ciordia, S. / Singer, A. / Kagan, O. / Egorova, O. / Alain Petit, P. / Stogios, P. / Kim, Y. / Tchigvintsev, A. / Flick, R. / Denaro, R. / Genovese, M. / Albar, J.P. / Reva, O.N. / Martinez-Gomariz, M. / Tran, H. / Ferrer, M. / Savchenko, A. / Yakunin, A.F. / Yakimov, M.M. / Golyshina, O.V. / Reinhardt, R. / Golyshin, P.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76 KB | Display | ![]() |
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PDB format | ![]() | 57 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.2 KB | Display | ![]() |
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Full document | ![]() | 435.5 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3i4qC ![]() 3iruC ![]() 3lmbC ![]() 3lnpC ![]() 3qvmC ![]() 3v77C ![]() 3vcrC ![]() 1onrS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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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
#1: Protein | Mass: 36288.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.88 Å3/Da / Density % sol: 74.77 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 4M sodium formate, 3mM magnesium chloride, cryoprotected in Paratone-N oil (Hampton), VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 27, 2009 / Details: Mirrors | |||||||||
Radiation | Monochromator: SI-111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→35.78 Å / Num. all: 18484 / Num. obs: 18469 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 26.2 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 57.4 | |||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 25.8 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.734 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1ONR Resolution: 2.79→35.78 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.472 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.269 / 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: 71.242 Å2
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Refinement step | Cycle: LAST / Resolution: 2.79→35.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.794→2.866 Å / Total num. of bins used: 20
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