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Open data
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Basic information
Entry | Database: PDB / ID: 4r56 | ||||||
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Title | Crystal structure of Sulfolobus Cren7-dsDNA(GTGATCAC) complex | ||||||
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![]() | DNA BINDING PROTEIN/DNA / BETA-SHEET / DNA BINDING / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() synthetic (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhang, Z.F. / Gong, Y. / Chen, Y.Y. / Li, H.B. / Huang, L. | ||||||
![]() | ![]() Title: Insights into the interaction between Cren7 and DNA: the role of loop beta 3-beta 4 Authors: Zhang, Z.F. / Gong, Y. / Chen, Y.Y. / Li, H.B. / Huang, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.3 KB | Display | ![]() |
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PDB format | ![]() | 37.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.6 KB | Display | ![]() |
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Full document | ![]() | 429.7 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4r55C ![]() 3lwhS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 6677.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 2426.617 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic (others) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 30% PEG 1500, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 16, 2010 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 14498 / Num. obs: 14194 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 37.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1354 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LWH Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.237 / ESU R Free: 0.193 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.169 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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