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- PDB-4do2: Crystal Structure of the Rop protein mutant D30P/A31G at resoluti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4do2 | ||||||
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Title | Crystal Structure of the Rop protein mutant D30P/A31G at resolution 1.4 resolution. | ||||||
![]() | Regulatory protein rop | ||||||
![]() | RNA BINDING PROTEIN / protein structure / protein folding / Rop protein / bacterial protein / mutation / 4-alpha-helical bundle / loop / ColE1 plasmid copy number | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Amprazi, M. / Kapetaniou, E.G. / Kokkinidis, M. | ||||||
![]() | ![]() Title: Structural plasticity of 4-alpha-helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein. Authors: Amprazi, M. / Kotsifaki, D. / Providaki, M. / Kapetaniou, E.G. / Fellas, G. / Kyriazidis, I. / Perez, J. / Kokkinidis, M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Purification, crystallization and preliminary X-ray diffraction analysis of a variant of the ColE1 Rop protein. Authors: Ambrazi, M. / Fellas, G. / Kapetaniou, E.G. / Kotsifaki, D. / Providaki, M. / Kokkinidis, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.5 KB | Display | ![]() |
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PDB format | ![]() | 27.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.7 KB | Display | ![]() |
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Full document | ![]() | 437.7 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 12.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ropS 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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Unit cell |
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Components
#1: Protein | Mass: 8163.035 Da / Num. of mol.: 2 / Mutation: D30P, A31G 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: 1.8 Å3/Da / Density % sol: 31.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 45%(v/v) methanol, 50 mM HEPES pH 6.4 and 100 mM Li2SO4, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 20, 2006 / Details: mirrors |
Radiation | Monochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.817 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→55.7 Å / Num. all: 22394 / Num. obs: 22394 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.4→1.45 Å / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ROP Resolution: 1.401→55.64 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 0.964 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 56.36 Å2 / Biso mean: 17.6643 Å2 / Biso min: 7.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.401→55.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.401→1.438 Å / Total num. of bins used: 20
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