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- PDB-4cxp: Structure of bifunctional endonuclease (AtBFN2) from Arabidopsis ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cxp | |||||||||
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Title | Structure of bifunctional endonuclease (AtBFN2) from Arabidopsis thaliana in complex with sulfate | |||||||||
![]() | ENDONUCLEASE 2 | |||||||||
![]() | HYDROLASE / ENDONUCLEASES / GLYCOSYLATION / SSDNA BINDING | |||||||||
Function / homology | ![]() T/G mismatch-specific endonuclease activity / Aspergillus nuclease S1 / double-stranded DNA endonuclease activity / single-stranded DNA endodeoxyribonuclease activity / DNA catabolic process / RNA endonuclease activity / endonuclease activity / nucleic acid binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yu, T.-F. / Maestre-Reyna, M. / Ko, C.-Y. / Ko, T.-P. / Sun, Y.-J. / Lin, T.-Y. / Shaw, J.-F. / Wang, A.H.-J. | |||||||||
![]() | ![]() Title: Structural Insights of the Ssdna Binding Site in the Multifunctional Endonuclease Atbfn2 from Arabidopsis Thaliana. Authors: Yu, T. / Maestre-Reyna, M. / Ko, C. / Ko, T. / Sun, Y. / Lin, T. / Shaw, J. / Wang, A.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.6 KB | Display | ![]() |
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PDB format | ![]() | 121.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 30 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cwmSC ![]() 4cxoC ![]() 4cxvC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30606.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 3 types, 3 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 497 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-1PE / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | OUR SEQUENCE CONTAINS A C-TERMINAL HISTIDINE TAG |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.33 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1 M HEPES PH 7.5, 0.2 M LI2SO4, 30% (W/V) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2012 / Details: MIRRORS |
Radiation | Monochromator: LN2-COOLED, FIXED-EXIT DOUBLE CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→50 Å / Num. obs: 107958 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 35.3 |
Reflection shell | Resolution: 1.22→1.26 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4CWM Resolution: 1.22→24.34 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.628 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.028 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.191 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→24.34 Å
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Refine LS restraints |
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