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Yorodumi- PDB-5oxx: Crystal structure of NeqN/NeqC complex from Nanoarcheaum equitans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oxx | ||||||
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Title | Crystal structure of NeqN/NeqC complex from Nanoarcheaum equitans at 1.7A | ||||||
Components |
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Keywords | SPLICING / Intein complex | ||||||
Function / homology | Function and homology information nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / 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 / MOLECULAR REPLACEMENT / Resolution: 1.74 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 | 5oxx.cif.gz | 58.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oxx.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 5oxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oxx_validation.pdf.gz | 427.5 KB | Display | wwPDB validaton report |
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Full document | 5oxx_full_validation.pdf.gz | 428.4 KB | Display | |
Data in XML | 5oxx_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 5oxx_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/5oxx ftp://data.pdbj.org/pub/pdb/validation_reports/ox/5oxx | HTTPS FTP |
-Related structure data
Related structure data | 5oxwSC 5oxzC S: Starting model for refinement C: citing same article (ref.) |
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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: 12316.899 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nanoarchaeum equitans (strain Kin4-M) (archaea) Strain: Kin4-M / Gene: NEQ068 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74N74 |
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#2: Protein/peptide | Mass: 3824.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nanoarchaeum equitans (strain Kin4-M) (archaea) Strain: Kin4-M / 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: 1.79 Å3/Da / Density % sol: 31.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% PEG3350 0,2M Ammonium Nitrate pH6.3 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→67.43 Å / Num. all: 158183 / Num. obs: 12621 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.023 / Rrim(I) all: 0.062 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.74→1.83 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1803 / CC1/2: 0.904 / Rpim(I) all: 0.39 / Rrim(I) all: 1.027 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OXW Resolution: 1.74→50.89 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.757 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.107 / 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: 37.318 Å2
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Refinement step | Cycle: 1 / Resolution: 1.74→50.89 Å
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Refine LS restraints |
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