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Yorodumi- PDB-2vkq: Crystal structure of human cytosolic 5'-nucleotidase III (cN-III,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vkq | ||||||
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Title | Crystal structure of human cytosolic 5'-nucleotidase III (cN-III, NT5C3) in complex with beryllium trifluoride | ||||||
Components | CYTOSOLIC 5'-NUCLEOTIDASE III | ||||||
Keywords | HYDROLASE / NUCLEOTIDASE / DISEASE MUTATION / HEMOLYTIC ANEMIA / PHOSPHOTRANSFERASE / NUCLEOTIDE-BINDING / ENDOPLASMIC RETICULUM / NUCLEOTIDE METABOLISM | ||||||
Function / homology | Function and homology information tRNA 2'-phosphotransferase activity / pyrimidine nucleoside metabolic process / 7-methylguanosine nucleotidase / Pyrimidine catabolism / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide metabolic process / defense response to virus / nuclear body ...tRNA 2'-phosphotransferase activity / pyrimidine nucleoside metabolic process / 7-methylguanosine nucleotidase / Pyrimidine catabolism / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide metabolic process / defense response to virus / nuclear body / nucleotide binding / magnesium ion binding / endoplasmic reticulum / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Wallden, K. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. ...Wallden, K. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Weigelt, J. / Welin, M. / Nordlund, P. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Cytosolic 5'- Nucleotidase III Authors: Wallden, K. / Stenmark, P. / Flodin, S. / Nyman, T. / Moche, M. / Ehn, M. / Hammarstrom, M. / Nilsson-Ehle, P. / Nordlund, P. #1: Journal: J.Biol.Chem. / Year: 2007 Title: Crystal Structure of Human Cytosolic 5'- Nucleotidase II: Insights Into Allosteric Regulation and Substrate Recognition Authors: Wallden, K. / Stenmark, P. / Nyman, T. / Flodin, S. / Graslund, S. / Loppnau, P. / Bianchi, V. / Nordlund, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vkq.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vkq.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vkq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vkq_validation.pdf.gz | 433.2 KB | Display | wwPDB validaton report |
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Full document | 2vkq_full_validation.pdf.gz | 435.5 KB | Display | |
Data in XML | 2vkq_validation.xml.gz | 12 KB | Display | |
Data in CIF | 2vkq_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/2vkq ftp://data.pdbj.org/pub/pdb/validation_reports/vk/2vkq | HTTPS FTP |
-Related structure data
Related structure data | 2cn1S 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
#1: Protein | Mass: 33199.020 Da / Num. of mol.: 1 / Fragment: RESIDUES 13-285 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): PGRO7 / References: UniProt: Q9H0P0, 5'-nucleotidase |
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#2: Chemical | ChemComp-BEF / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.5 % / Description: NONE |
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Crystal grow | Details: 24% PEG1500, 20% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94 |
Detector | Date: Feb 25, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→78.09 Å / Num. obs: 12172 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CN1 Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU B: 19.036 / SU ML: 0.207 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.488 / ESU R Free: 0.27 / 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: 46.09 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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