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- PDB-2xcv: Crystal structure of the D52N variant of cytosolic 5'-nucleotidas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xcv | ||||||
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Title | Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with inosine monophosphate and 2,3-bisphosphoglycerate | ||||||
![]() | CYTOSOLIC PURINE 5'-NUCLEOTIDASE | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wallden, K. / Nordlund, P. | ||||||
![]() | ![]() Title: Structural Basis for the Allosteric Regulation and Substrate Recognition of Human Cytosolic 5'-Nucleotidase II Authors: Wallden, K. / Nordlund, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.1 KB | Display | ![]() |
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PDB format | ![]() | 90.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xcwC ![]() 2xcxC ![]() 2xjbC ![]() 2xjcC ![]() 2xjdC ![]() 2xjeC ![]() 2xjfC ![]() 2jcmS 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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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 63956.750 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 262 molecules ![](data/chem/img/DG2.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/IMP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/IMP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DG2 / (![]() |
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#3: Chemical | ChemComp-GOL / ![]() |
#4: Chemical | ChemComp-IMP / ![]() |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / ![]() |
-Details
Compound details | ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2008 / Details: DYNAMICALLY BENDABLE |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→20 Å / Num. obs: 34216 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.6 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2JCM Resolution: 2.3→48.68 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.283 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 35.669 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→48.68 Å
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Refine LS restraints |
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