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Yorodumi- PDB-3qqz: Crystal structure of the C-terminal domain of the yjiK protein fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qqz | ||||||
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Title | Crystal structure of the C-terminal domain of the yjiK protein from Escherichia coli CFT073 | ||||||
Components | Putative uncharacterized protein yjiK | ||||||
Keywords | METAL BINDING PROTEIN / MCSG / PSI-2 / Structural Genomics / Midwest Center for Structural Genomics / TolB-like / uncharacterized protein / Ca binding / Protein Structure Initiative | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å | ||||||
Authors | Stein, A. / Chhor, G. / Nocek, B. / Fenske, R.J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of the C-terminal domain of the yjiK protein from Escherichia coli CFT073 Authors: Stein, A. / Chhor, G. / Nocek, B. / Fenske, R.J. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qqz.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qqz.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 3qqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qqz_validation.pdf.gz | 426.3 KB | Display | wwPDB validaton report |
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Full document | 3qqz_full_validation.pdf.gz | 430.2 KB | Display | |
Data in XML | 3qqz_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 3qqz_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/3qqz ftp://data.pdbj.org/pub/pdb/validation_reports/qq/3qqz | 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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Details | THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Components
#1: Protein | Mass: 28621.529 Da / Num. of mol.: 1 / Fragment: C-terminal domain residues 35-286 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ABU 83972 / Gene: yjiK, ECABU_c49710 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: E1PG53 | ||
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#2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M sodium Cacodylate, 0.2 M Calcium Acetate, 40% Peg 300, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 30, 2010 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→40 Å / Num. all: 12816 / Num. obs: 12816 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 37 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.55→40 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.896 / SU B: 9.614 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.388 / ESU R Free: 0.3 / 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: 39.673 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.551→2.617 Å / Total num. of bins used: 20
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