+Open data
-Basic information
Entry | Database: PDB / ID: 2iji | ||||||
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Title | Structure of F14H mutant of ColE1 Rom protein | ||||||
Components | Regulatory protein rop | ||||||
Keywords | TRANSCRIPTION REGULATOR / Rom / Rop / ColE1 plasmid copy control | ||||||
Function / homology | Helix Hairpins - #230 / Regulatory protein Rop / Rop-like superfamily / Rop protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / identical protein binding / Regulatory protein rop Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Struble, E.B. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: New crystal structures of ColE1 Rom and variants resulting from mutation of a surface exposed residue: Implications for RNA-recognition. Authors: Struble, E.B. / Ladner, J.E. / Brabazon, D.M. / Marino, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iji.cif.gz | 22.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iji.ent.gz | 14.3 KB | Display | PDB format |
PDBx/mmJSON format | 2iji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/2iji ftp://data.pdbj.org/pub/pdb/validation_reports/ij/2iji | HTTPS FTP |
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-Related structure data
Related structure data | 2ijhC 2ijjC 2ijkC 1ropS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7153.868 Da / Num. of mol.: 1 / Mutation: M1G, F14H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rop / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P03051 |
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#2: 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: 1.78 Å3/Da / Density % sol: 30.72 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1uL protein solution (0.5-1 mM) was mixed with 1 uL well buffer (0.1M sodium acetate pH 5.5, 0.1M sodium chloride, 37 40% ethanol, and 20% glycerol), VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 12, 2005 / Details: Blue Max-flux confocal mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→33.1 Å / Num. obs: 2378 / % possible obs: 96.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.44 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 2.3 / Num. unique all: 222 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ROP Resolution: 2.3→33.1 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.911 / SU B: 14.505 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 0.664 / ESU R Free: 0.323 / 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: 46.312 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→33.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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