+Open data
-Basic information
Entry | Database: PDB / ID: 2ijh | ||||||
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Title | Crystal structure analysis of ColE1 ROM mutant F14W | ||||||
Components | Regulatory protein rop | ||||||
Keywords | TRANSCRIPTION REGULATOR / rop / rom / colE1 / RNA-recognition | ||||||
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: 1.8 Å | ||||||
Authors | Ladner, J.E. | ||||||
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 | 2ijh.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ijh.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ijh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ijh_validation.pdf.gz | 440.5 KB | Display | wwPDB validaton report |
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Full document | 2ijh_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 2ijh_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 2ijh_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/2ijh ftp://data.pdbj.org/pub/pdb/validation_reports/ij/2ijh | HTTPS FTP |
-Related structure data
Related structure data | 2ijiC 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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2 |
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Unit cell |
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Details | Chains A and B form one biological dimer. / Chain C forms half of a second dimer. The other chain is generated by the two fold axis -x,-y,z and translation of one unit cell along the a axis. |
-Components
#1: Protein | Mass: 7201.932 Da / Num. of mol.: 3 / Mutation: M1G, F14W 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 #2: 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: 2.43 Å3/Da / Density % sol: 49.36 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Well solution: 20% glycerol, 0.1 M sodium acetate pH 5.5, 0.1 M sodium chloride. Protein solution: protein 5 mg/ml, 0.01 M Tris pH 6.8, 0.05 M sodium chloride. Drops: equal volumes of well ...Details: Well solution: 20% glycerol, 0.1 M sodium acetate pH 5.5, 0.1 M sodium chloride. Protein solution: protein 5 mg/ml, 0.01 M Tris pH 6.8, 0.05 M sodium chloride. Drops: equal volumes of well and protein solutions., VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-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: Jan 20, 2005 / Details: Blue Max-flux confocal |
Radiation | Monochromator: confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.97 Å / Num. all: 20287 / Num. obs: 20252 / % possible obs: 99.8 % / Redundancy: 3.24 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1950 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ROP Resolution: 1.8→19.97 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.683 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.529 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.897 Å / Total num. of bins used: 10
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