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Yorodumi- PDB-5oxz: Crystal Structure of NeqN/NeqC complex from Nanoarcheaum equitans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oxz | ||||||
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Title | Crystal Structure of NeqN/NeqC complex from Nanoarcheaum equitans at 1.2A | ||||||
Components |
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Keywords | SPLICING / Intein complex 1 | ||||||
Function / homology | Function and homology information DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | Nanoarchaeum equitans (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.2 Å | ||||||
Authors | Aparicio, D. / Perez-Luque, R. / Ribo, M. / Fita, I. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2018 Title: Structural Insights into Subunits Assembly and the Oxyester Splicing Mechanism of Neq pol Split Intein. Authors: Gordo, V. / Aparicio, D. / Perez-Luque, R. / Benito, A. / Vilanova, M. / Uson, I. / Fita, I. / Ribo, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oxz.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oxz.ent.gz | 60.9 KB | Display | PDB format |
PDBx/mmJSON format | 5oxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/5oxz ftp://data.pdbj.org/pub/pdb/validation_reports/ox/5oxz | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12299.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nanoarchaeum equitans (strain Kin4-M) (archaea) Gene: NEQ068 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74N74 |
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#2: Protein/peptide | Mass: 3818.362 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nanoarchaeum equitans (strain Kin4-M) (archaea) Gene: NEQ528 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74M37 |
#3: 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: 2.37 Å3/Da / Density % sol: 48.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.1 M Di-Ammonium Tartrate pH7 |
-Data collection
Diffraction | Mean temperature: 78 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97929 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→42.41 Å / Num. obs: 51160 / % possible obs: 99.9 % / Redundancy: 12.2 % / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.2→42.4 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.901 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.092 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→42.4 Å
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Refine LS restraints |
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