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Yorodumi- PDB-3bed: Mannose/sorbose specific IIA subunit of phosphotransferase system... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bed | |||||||||
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Title | Mannose/sorbose specific IIA subunit of phosphotransferase system from Enterococcus faecalis | |||||||||
Components | PTS system, IIA component | |||||||||
Keywords | TRANSFERASE / MANNOSE/SORBOSE / PHOSPHOTRANSFERASE SYSTEM / STRUCTURAL GENOMICS / APC28805 / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG | |||||||||
Function / homology | Function and homology information phosphoenolpyruvate-dependent sugar phosphotransferase system / transferase activity / membrane => GO:0016020 Similarity search - Function | |||||||||
Biological species | Enterococcus faecalis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å | |||||||||
Authors | Osipiuk, J. / Wu, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | |||||||||
Citation | Journal: To be Published Title: X-Ray Crystal Structure of Mannose/sorbose specific IIa subunit of phosphotransferase system from Enterococcus faecalis. Authors: Osipiuk, J. / Wu, R. / Moy, S. / Joachimiak, A. | |||||||||
History |
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Remark 999 | SEQUENCE LYSINE RESIDUES OF THE PROTEIN WERE CHEMICALLY DIMETHYLATED AFTER PROTEIN PURIFICATION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bed.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bed.ent.gz | 102.5 KB | Display | PDB format |
PDBx/mmJSON format | 3bed.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/3bed ftp://data.pdbj.org/pub/pdb/validation_reports/be/3bed | 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 on special symmetry positions |
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Details | Authors state that the biological unit of this protein is unknown. |
-Components
#1: Protein | Mass: 15304.130 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_0461 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q838I6 #2: 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: 2.13 Å3/Da / Density % sol: 42.33 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M CALCIUM CHLORIDE, 0.1 M HEPES BUFFER, 30% PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 6, 2006 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→37.5 Å / Num. all: 36836 / Num. obs: 36836 / % possible obs: 79.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 35.3 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.18 / Num. unique all: 973 / % possible all: 31.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.45→37.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.626 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.104 / ESU R Free: 0.081 / 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: 24.158 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→37.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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