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Open data
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Basic information
Entry | Database: PDB / ID: 4huf | ||||||
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Title | Structure of 5-chlorouracil modified A:U base pair | ||||||
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![]() | Hydrolase/DNA / 5-chloro-2'-deoxyuridine / W-C base pair / Wobble base pair / double helix / Watson-Crick base pairing pattern / Hydrolase-DNA complex | ||||||
Function / homology | ![]() ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patra, A. / Egli, M. | ||||||
![]() | ![]() Title: Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs. Authors: Patra, A. / Harp, J. / Pallan, P.S. / Zhao, L. / Abramov, M. / Herdewijn, P. / Egli, M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.1 KB | Display | ![]() |
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PDB format | ![]() | 76.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4htuC ![]() 4hueC ![]() 4hugC ![]() 3d0pS C: citing same article ( 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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2 | ![]()
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Unit cell |
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Components
-Protein / DNA chain , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 15429.371 Da / Num. of mol.: 2 / Mutation: D132N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125 Gene: BH0863, rnhA / Production host: ![]() ![]() #2: DNA chain | Mass: 3683.811 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Dickerson Dodecamer DNA, ClU7 |
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-Non-polymers , 4 types, 456 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate (pH 6.5) and 20% (w/v) PEG 8000 , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 11, 2011 | ||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.69→50 Å / Num. all: 54372 / Num. obs: 54315 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % | ||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3D0P Resolution: 1.69→35.896 Å / SU ML: 0.17 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 5 / Phase error: 21.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→35.896 Å
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Refine LS restraints |
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LS refinement shell |
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