+Open data
-Basic information
Entry | Database: PDB / ID: 4kl6 | ||||||
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Title | Crystal structure of dimeric form of NpuDnaE intein | ||||||
Components | DNA-directed DNA polymerase,Nucleic acid binding, OB-fold, tRNA/helicase-type | ||||||
Keywords | UNKNOWN FUNCTION / HINT / intein / domain swapped / NpuDnaE inten | ||||||
Function / homology | Function and homology information intein-mediated protein splicing / 3'-5' exonuclease activity / helicase activity / DNA replication / nucleic acid binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity Similarity search - Function | ||||||
Biological species | Nostoc punctiforme (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Aranko, A.S. / Oeemig, J.S. / Kajander, T. / Iwai, H. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2013 Title: Intermolecular domain swapping induces intein-mediated protein alternative splicing. Authors: Aranko, A.S. / Oeemig, J.S. / Kajander, T. / Iwai, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kl6.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kl6.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 4kl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/4kl6 ftp://data.pdbj.org/pub/pdb/validation_reports/kl/4kl6 | HTTPS FTP |
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-Related structure data
Related structure data | 4kl5C 2keqS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15605.601 Da / Num. of mol.: 4 Fragment: NpuDnaE Intein (unp residues 775-876, unp residues 2-37) Mutation: C775A, C37S,C775A, C37S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: ATCC 29133 / PCC 73102 / Gene: Npun_F4872, Npun_F5684 / Plasmid: pHYRSF236 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 References: UniProt: B2J066, UniProt: B2J821, DNA-directed DNA polymerase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris, 2.0 M ammonium phosphate , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2010 / Details: monochromator crystals | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. all: 29589 / Num. obs: 27269 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.068 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2KEQ Resolution: 2.2→19.976 Å / SU ML: 0.34 / σ(F): 2 / σ(I): 2 / Phase error: 27.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.144 Å2 / ksol: 0.37 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.976 Å
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Refine LS restraints |
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LS refinement shell |
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