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Yorodumi- PDB-3kao: Crystal structure of tagatose 1,6-diphosphate aldolase from Staph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kao | ||||||
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Title | Crystal structure of tagatose 1,6-diphosphate aldolase from Staphylococcus aureus | ||||||
Components | Tagatose 1,6-diphosphate aldolase | ||||||
Keywords | LYASE / tagatose 1 / 6-diphosphate aldolase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Lactose metabolism | ||||||
Function / homology | Function and homology information 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 | Staphylococcus aureus subsp. aureus Mu50 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Chang, C. / Marshall, N. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of tagatose 1,6-diphosphate aldolase from Staphylococcus aureus Authors: Chang, C. / Marshall, N. / Cobb, G. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kao.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kao.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 3kao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kao_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 3kao_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 3kao_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 3kao_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/3kao ftp://data.pdbj.org/pub/pdb/validation_reports/ka/3kao | HTTPS FTP |
-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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37146.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria) Strain: Mu50 / ATCC 700699 Gene: lacD, SAV2192, Staphylococcus aureus subsp. aureus Mu50 Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)magic / References: UniProt: P0A009, tagatose-bisphosphate aldolase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.9 Å3/Da / Density % sol: 74.87 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10 mM zinc sulfate, 100 mM MES pH 6.5, 12.5 % PEG550 MME, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2009 |
Radiation | Monochromator: Si(111)double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 59080 / Num. obs: 59016 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 54.7 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 6.43 / Num. unique all: 2889 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.355 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.079 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.146 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 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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