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- PDB-2xjc: 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: 2xjc | ||||||
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Title | Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with guanosine monophosphate and diadenosine tetraphosphate | ||||||
![]() | 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 | ![]() | 223.5 KB | Display | ![]() |
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PDB format | ![]() | 177.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xcvC ![]() 2xcwC ![]() 2xcxC ![]() 2xjbC ![]() 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 63956.750 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-536 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 405 molecules ![](data/chem/img/5GP.gif)
![](data/chem/img/B4P.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/B4P.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-5GP / ![]() | ||||
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#3: Chemical | ChemComp-B4P / ![]() | ||||
#4: Chemical | ChemComp-GOL / ![]() #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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Crystal grow![]() | Details: 0.1 M BICINE PH 9.0, 10% PEG6000 |
-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→20 Å / Num. obs: 51649 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.37 |
Reflection shell | Resolution: 2→2.2 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2JCM Resolution: 2→45.79 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.316 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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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: 33.892 Å2
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Refinement step | Cycle: LAST / Resolution: 2→45.79 Å
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Refine LS restraints |
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