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Yorodumi- PDB-3mgl: Crystal structure of permease family protein from Vibrio cholerae -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mgl | ||||||
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Title | Crystal structure of permease family protein from Vibrio cholerae | ||||||
Components | Sulfate permease family protein | ||||||
Keywords | TRANSPORT PROTEIN / PSI2 / MCSG / structural genomics / sulfate permease family protein / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information inorganic anion transmembrane transport / fumarate transmembrane transporter activity / fumarate transport / succinate transmembrane transport / succinate transmembrane transporter activity / L-aspartate transmembrane transporter activity / monoatomic anion transmembrane transporter activity / membrane Similarity search - Function | ||||||
Biological species | Vibrio cholerae O1 biovar El Tor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å | ||||||
Authors | Chang, C. / Marshall, N. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of permease family protein from Vibrio cholerae Authors: Chang, C. / Marshall, N. / Bearden, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mgl.cif.gz | 108.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mgl.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 3mgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/3mgl ftp://data.pdbj.org/pub/pdb/validation_reports/mg/3mgl | 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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Unit cell |
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Details | octamer with operator (x,y,z), (y-1/2,-x+3/2,z), (-y+3/2,x+1/2,z), (-x+1,-y+2,z) |
-Components
#1: Protein | Mass: 14596.197 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria) Strain: N16961 / Gene: VC_A0077 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9KN88 #2: Chemical | ChemComp-IOD / #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: 2.31 Å3/Da / Density % sol: 46.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Potassium iodide, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2010 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 13528 / Num. obs: 13508 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 63.7 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 12.2 / Num. unique all: 656 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.864 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.23 / 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: 28.258 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.249→2.308 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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