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- PDB-3lfp: Crystal Structure of the Restriction-Modification Controller Prot... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lfp | ||||||
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Title | Crystal Structure of the Restriction-Modification Controller Protein C.Csp231I | ||||||
![]() | Csp231I C protein | ||||||
![]() | TRANSCRIPTION / transcriptional regulator / DNA binding protein / helix-turn-helix / restriction-modification | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | McGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G. | ||||||
![]() | ![]() Title: Structural Analysis of a Novel Class of R-M Controller Proteins: C.Csp231I from Citrobacter sp. RFL231. Authors: McGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Taylor, J.E. / Shevtsov, M.B. / Kneale, G.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 32.7 KB | Display | ![]() |
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PDB format | ![]() | 23.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.8 KB | Display | ![]() |
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Full document | ![]() | 424.8 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 8.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lisC ![]() 1y7yS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11380.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.16 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Na HEPES, 1.4M Tri-sodium citrate dihydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2009 |
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 7979 / Num. obs: 7753 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 38.7 % / Biso Wilson estimate: 35.293 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 42.78 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 38.8 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 11.3 / Num. measured obs: 42928 / Num. unique all: 991 / Num. unique obs: 1052 / % possible all: 94.2 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1Y7Y Resolution: 2→19.24 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.172 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.871 / SU B: 2.794 / SU ML: 0.083 / SU R Cruickshank DPI: 0.162 / SU Rfree: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.154 / 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: 115.25 Å2 / Biso mean: 41.169 Å2 / Biso min: 16.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.053 Å / Total num. of bins used: 20
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