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- PDB-4x4f: RADIATION DAMAGE TO THE NUCLEOPROTEIN COMPLEX C.Esp1396I: DOSE (D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4x4f | ||||||
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Title | RADIATION DAMAGE TO THE NUCLEOPROTEIN COMPLEX C.Esp1396I: DOSE (DWD) 20.6 MGy | ||||||
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![]() | GENE REGULATION / protein-DNA complex / radiation damage | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Bury, C.S. / McGeehan, J.E. / Garman, E.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Radiation damage to nucleoprotein complexes in macromolecular crystallography. Authors: Bury, C. / Garman, E.F. / Ginn, H.M. / Ravelli, R.B. / Carmichael, I. / Kneale, G. / McGeehan, J.E. #1: ![]() Title: Structural analysis of the genetic switch that regulates the expression of restriction-modification genes. Authors: McGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Ball, N. / Ravelli, R.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 | ![]() | 112.1 KB | Display | ![]() |
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PDB format | ![]() | 83.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.2 KB | Display | ![]() |
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Full document | ![]() | 469.1 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 20.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4x4bC ![]() 4x4cC ![]() 4x4dC ![]() 4x4eC ![]() 4x4gC ![]() 4x4hC ![]() 4x4iC ![]() 3clcS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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Details | biological unit is the same as asym. |
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Components
#1: Protein | Mass: 9521.175 Da / Num. of mol.: 4 / Fragment: Controller protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | | Mass: 10791.966 Da / Num. of mol.: 1 / Fragment: Operator DNA / Source method: obtained synthetically / Details: Chemically synthesised DNA / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 10738.960 Da / Num. of mol.: 1 / Fragment: Operator DNA / Source method: obtained synthetically / Details: Chemically synthesised DNA / Source: (synth.) synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.51 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: MES, MPD, MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2007 | |||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9322 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.8→69.59 Å / Num. obs: 21207 / % possible obs: 99.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 65.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.023 / Net I/σ(I): 22.6 / Num. measured all: 128476 / Scaling rejects: 132 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CLC Resolution: 2.8→19.039 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.29 / 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 max: 143.48 Å2 / Biso mean: 66.4485 Å2 / Biso min: 31.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→19.039 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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