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- PDB-2xjf: 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: 2xjf | ||||||
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Title | Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II with a covalently modified Asn52 | ||||||
![]() | 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 | ![]() | 117.4 KB | Display | ![]() |
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PDB format | ![]() | 88.2 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 ![]() 2xjcC ![]() 2xjdC ![]() 2xjeC ![]() 2jc9S 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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Unit cell |
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Components
#1: Protein | Mass: 64131.953 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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#2: Chemical | ChemComp-DG2 / (![]() | ||||||
#3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Nonpolymer details | THE IDENTITY OF THE CARBOXY GROUP OF ASN52 (A5N) IS UNCERTAIN | Sequence details | ASP52 MUTATED TO AN ASPARAGINE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.5 % / Description: NONE |
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Crystal grow![]() | Details: 0.1 M BICINE PH 9.0, 10% PEG 6000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→50 Å / Num. obs: 43556 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.9 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2JC9 Resolution: 2.1→65.23 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.573 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.154 / 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: 25.414 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→65.23 Å
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Refine LS restraints |
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