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Yorodumi- PDB-4ew5: C-terminal domain of inner membrane protein CigR from Salmonella ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ew5 | ||||||
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Title | C-terminal domain of inner membrane protein CigR from Salmonella enterica. | ||||||
Components | CigR Protein | ||||||
Keywords | MEMBRANE PROTEIN / inner membrane protein / structural genomics / APC101781 / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Program for the Characterization of Secreted Effector Proteins / PCSEP | ||||||
Function / homology | inner membrane protein cigr / Nuclear Transport Factor 2; Chain: A, / membrane => GO:0016020 / Roll / Alpha Beta / CigR Function and homology information | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å | ||||||
Authors | Osipiuk, J. / Xu, X. / Cui, H. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Niemann, G.S. / Merkley, E.D. / Savchenko, A. ...Osipiuk, J. / Xu, X. / Cui, H. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Niemann, G.S. / Merkley, E.D. / Savchenko, A. / Adkins, J.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP) | ||||||
Citation | Journal: To be Published Title: C-terminal domain of inner membrane protein CigR from Salmonella enterica. Authors: Osipiuk, J. / Xu, X. / Cui, H. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Niemann, G.S. / Merkley, E.D. / Savchenko, A. / Adkins, J.N. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ew5.cif.gz | 87.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ew5.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ew5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/4ew5 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/4ew5 | 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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-Components
#1: Protein | Mass: 10894.444 Da / Num. of mol.: 2 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: cigR, STM3762 / Plasmid: pET21b-L No TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z621 #2: Chemical | #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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Hepes buffer, 2% PEG-400, 2M Ammonium sulphate. Full length protein was crystallized in presence of V8 protease., pH 7.5, 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: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.87→41.4 Å / Num. all: 17270 / Num. obs: 17270 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.107 / Χ2: 2.551 / Net I/σ(I): 8.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.87→41.4 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.798 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.14 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 75.97 Å2 / Biso mean: 31.4572 Å2 / Biso min: 17.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→41.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.872→1.92 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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