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Yorodumi- PDB-4er9: Crystal structure of cytochrome b562 from Salmonella enterica sub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4er9 | ||||||
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Title | Crystal structure of cytochrome b562 from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S | ||||||
Components | Soluble cytochrome b562 | ||||||
Keywords | ELECTRON TRANSPORT / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG / Program for the Characterization of Secreted Effector Proteins / PCSEP | ||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.897 Å | ||||||
Authors | Tan, K. / Hatzos-Skintges, C. / Jedrzejczak, R. / Adkins, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP) | ||||||
Citation | Journal: To be Published Title: Crystal structure of cytochrome b562 from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S Authors: Tan, K. / Hatzos-Skintges, C. / Jedrzejczak, R. / Adkins, 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 | 4er9.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4er9.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 4er9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/4er9 ftp://data.pdbj.org/pub/pdb/validation_reports/er/4er9 | 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 | Experimentally unknown. It is predicted to be monomeric. |
-Components
#1: Protein | Mass: 14206.278 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: 14028S / Gene: cybC, STM4439 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: P63727 | ||||
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#2: Chemical | ChemComp-PEG / | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #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: 2.64 Å3/Da / Density % sol: 53.38 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 3.5M Ammonium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97909 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2011 / Details: Mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97909 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41 Å / Num. all: 11910 / Num. obs: 11910 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 54.8 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 2.74 / Num. unique all: 529 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.897→40.846 Å / SU ML: 0.5 / σ(F): 0 / Phase error: 33.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.006 Å2 / ksol: 0.362 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.897→40.846 Å
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Refine LS restraints |
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LS refinement shell |
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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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