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Open data
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Basic information
Entry | Database: PDB / ID: 2ijj | ||||||
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Title | Crystal structure analysis of ColE1 ROM mutant F14Y | ||||||
![]() | Regulatory protein rop | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ladner, J.E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.3 KB | Display | ![]() |
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PDB format | ![]() | 35.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.7 KB | Display | ![]() |
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Full document | ![]() | 443.1 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ijhC ![]() 2ijiC ![]() 2ijkC ![]() 1ropS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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. |
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Components
#1: Protein | Mass: 7178.896 Da / Num. of mol.: 3 / Mutation: M1G, F14Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Well solution: 22% MPD, 0.1 M sodium acetate pH 5.5, 0.1 M sodium chloride. Protein solution: protein 2.5 mg/ml, 0.01 M Tris pH 6.5, 0.05 M sodium chloride. Drops: equal volumes of well and ...Details: Well solution: 22% MPD, 0.1 M sodium acetate pH 5.5, 0.1 M sodium chloride. Protein solution: protein 2.5 mg/ml, 0.01 M Tris pH 6.5, 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: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 3, 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: 1.89→20.01 Å / Num. all: 17596 / Num. obs: 17351 / % possible obs: 98.6 % / Redundancy: 4.94 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.89→1.96 Å / Redundancy: 4.69 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1707 / % possible all: 93.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ROP Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.117 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.156 / 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: 30.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.895→1.997 Å / Total num. of bins used: 10
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