+Open data
-Basic information
Entry | Database: PDB / ID: 2ivn | ||||||
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Title | Structure of UP1 protein | ||||||
Components | O-SIALOGLYCOPROTEIN ENDOPEPTIDASE | ||||||
Keywords | HYDROLASE / UP1 KEOPS COMPLEX / FE/ZN DEPENDENT NUCLEOTIDE PHOSPHATASE / METALLOPROTEASE / HYPOTHETICAL PROTEIN / ZINC / PROTEASE / METAL-BINDING | ||||||
Function / homology | Function and homology information N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / tRNA binding / single-stranded RNA binding / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | PYROCOCCUS ABYSSI (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Hecker, A. / Leulliot, N. / Graille, M. / Dorlet, P. / Quevillon-Cheruel, S. / Ulryck, N. / Van Tilbeurgh, H. / Forterre, P. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2007 Title: An Archaeal Orthologue of the Universal Protein Kae1 is an Iron Metalloprotein which Exhibits Atypical DNA-Binding Properties and Apurinic-Endonuclease Activity in Vitro. Authors: Hecker, A. / Leulliot, N. / Gadelle, D. / Graille, M. / Justome, A. / Dorlet, P. / Brochier, C. / Quevillon-Cheruel, S. / Le Cam, E. / Van Tilbeurgh, H. / Forterre, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ivn.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ivn.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ivn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/2ivn ftp://data.pdbj.org/pub/pdb/validation_reports/iv/2ivn | HTTPS FTP |
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-Related 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: 36244.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS ABYSSI (archaea) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA (DE3) PLYSS / References: UniProt: Q9UXT7, EC: 3.4.24.57 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-ANP / |
#4: Chemical | ChemComp-MG / |
#5: 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: 2.14 Å3/Da / Density % sol: 41.95 % / Description: NONE |
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Crystal grow | pH: 5.6 / Details: 25% PEG 4000, 0.3M KCL, 0.1M SODIUM CITRATE PH5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. obs: 41853 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 2.84 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.029 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.102 / 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: 21.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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