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Yorodumi- PDB-2xjd: Crystal structure of the D52N variant of cytosolic 5'-nucleotidas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xjd | ||||||
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Title | Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with inorganic phosphate and deoxyadenosine triphosphate | ||||||
Components | CYTOSOLIC PURINE 5'-NUCLEOTIDASE | ||||||
Keywords | HYDROLASE / ALLOSTERIC ENZYME / CN-II / GMP-IMP SPECIFIC NUCLEOTIDASE / HIGH KM 5-PRIME NUCLEOTIDASE / METAL-BINDING / NT5C2 / NUCLEOTIDE METABOLISM / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN | ||||||
Function / homology | Function and homology information nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity ...nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / Ribavirin ADME / IMP metabolic process / IMP catabolic process / Purine catabolism / allantoin metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wallden, K. / Nordlund, P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Structural Basis for the Allosteric Regulation and Substrate Recognition of Human Cytosolic 5'-Nucleotidase II. Authors: Wallden, K. / Nordlund, P. #1: Journal: J.Mol.Biol. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xjd.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xjd.ent.gz | 93.5 KB | Display | PDB format |
PDBx/mmJSON format | 2xjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xjd_validation.pdf.gz | 860.9 KB | Display | wwPDB validaton report |
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Full document | 2xjd_full_validation.pdf.gz | 865.1 KB | Display | |
Data in XML | 2xjd_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 2xjd_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/2xjd ftp://data.pdbj.org/pub/pdb/validation_reports/xj/2xjd | HTTPS FTP |
-Related structure data
Related structure data | 2xcvC 2xcwC 2xcxC 2xjbC 2xjcC 2xjeC 2xjfC 2jcmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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 / Fragment: RESIDUES 1-536 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P49902, 5'-nucleotidase |
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-Non-polymers , 5 types, 468 molecules
#2: Chemical | ChemComp-ATP / | ||||||
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#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PO4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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, 10% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 2, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2→65.65 Å / Num. obs: 52910 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.54 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JCM Resolution: 2→64.28 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.78 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.125 / 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: 20.596 Å2
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Refinement step | Cycle: LAST / Resolution: 2→64.28 Å
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