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- PDB-3myp: Crystal structure of tagatose-1,6-bisphosphate aldolase from Stap... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3myp | ||||||
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Title | Crystal structure of tagatose-1,6-bisphosphate aldolase from Staphylococcus aureus | ||||||
![]() | Tagatose 1,6-diphosphate aldolase | ||||||
![]() | LYASE / beta-alpha-barrel | ||||||
Function / homology | ![]() tagatose-bisphosphate aldolase / lactose catabolic process via tagatose-6-phosphate / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity / tagatose-bisphosphate aldolase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, S.J. / Kim, H.S. / Kim, D.J. / Yoon, H.J. / Kim, K.H. / Yoon, J.Y. / Suh, S.W. | ||||||
![]() | ![]() Title: Crystal structures of LacD from Staphylococcus aureus and LacD.1 from Streptococcus pyogenes: Insights into substrate specificity and virulence gene regulation Authors: Lee, S.J. / Kim, H.S. / Kim, D.J. / Yoon, H.J. / Kim, K.H. / Yoon, J.Y. / Suh, S.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 249.8 KB | Display | ![]() |
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PDB format | ![]() | 212.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.6 KB | Display | ![]() |
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Full document | ![]() | 481.7 KB | Display | |
Data in XML | ![]() | 46.8 KB | Display | |
Data in CIF | ![]() | 65 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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: 37944.980 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.25 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M calcium chloride, 0.1M HEPES, 28% (v/v) PEG 400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 4, 2008 |
Radiation | Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.989→20 Å / Num. obs: 28654 / Redundancy: 17.3 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 2.989→3.05 Å / Redundancy: 15.4 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1379 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.99→19.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.989→3.065 Å / Total num. of bins used: 20
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