+Open data
-Basic information
Entry | Database: PDB / ID: 2ivp | ||||||
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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 / SAD / Resolution: 2.5 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 | 2ivp.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ivp.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ivp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/2ivp ftp://data.pdbj.org/pub/pdb/validation_reports/iv/2ivp | 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-FE2 / |
#3: Chemical | ChemComp-ATP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.17 % / Description: NONE |
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Crystal grow | pH: 5.6 / Details: pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.74005 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.74005 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 11607 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 13.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→10 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.89 / SU B: 10.86 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 2.914 / ESU R Free: 0.358 / 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: 33.52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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