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Open data
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Basic information
Entry | Database: PDB / ID: 4i8t | ||||||
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Title | C.Esp1396I bound to a 19 base pair DNA duplex | ||||||
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![]() | Transcription/DNA / Restriction-modification / helix-turn-helix / transcriptional regulator / DNA / Transcription-DNA complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Martin, R.N.A. / McGeehan, J.E. / Kneale, G.G. | ||||||
![]() | ![]() Title: Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I. Authors: Martin, R.N. / McGeehan, J.E. / Ball, N.J. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G. #1: ![]() Title: Structure of the restriction-modification controller protein C.Esp1396I. Authors: Ball, N. / Streeter, S.D. / Kneale, G.G. / McGeehan, J.E. #2: ![]() Title: Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex. Authors: McGeehan, J.E. / Ball, N.J. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G. #3: ![]() Title: The structural basis of differential DNA sequence recognition by restriction-modification controller proteins. Authors: Ball, N.J. / McGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G. #4: ![]() Title: Structure of the restriction-modification controller protein C.Esp1396I. Authors: Ball, N. / Streeter, S.D. / Kneale, G.G. / McGeehan, J.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.6 KB | Display | ![]() |
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PDB format | ![]() | 45.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.1 KB | Display | ![]() |
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Full document | ![]() | 450.9 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4iwrC ![]() 3g5gS 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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Unit cell |
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Components
#1: Protein | Mass: 9521.175 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | | Mass: 5787.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesised DNA Oligonucleotide #3: DNA chain | | Mass: 5858.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesised DNA Oligonucleotide |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M PCTP buffer, 25 % w/v PEG 1500, 10 mM Spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2011 |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979493 Å / Relative weight: 1 |
Reflection | Resolution: 3→73.702 Å / Num. all: 22560 / Num. obs: 6809 / % possible obs: 99.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 3→3.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.013 / Mean I/σ(I) obs: 0.9 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3G5G Resolution: 3→44.434 Å / Occupancy max: 1 / Occupancy min: 0.14 / SU ML: 0.34 / σ(F): 1.91 / Phase error: 32.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 104.5102 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→44.434 Å
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Refine LS restraints |
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