+Open data
-Basic information
Entry | Database: PDB / ID: 6qm2 | ||||||
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Title | NlaIV restriction endonuclease | ||||||
Components | Type-2 restriction enzyme NlaIV | ||||||
Keywords | HYDROLASE / RESTRICTION ENDONUCLEASE / NLAIV / BLUNT END CUTTER | ||||||
Function / homology | Type-2 restriction enzyme NlaIV / NgoBV restriction endonuclease / type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / : / Type-2 restriction enzyme NlaIV Function and homology information | ||||||
Biological species | Neisseria lactamica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Czapinska, H. / Siwek, W. / Szczepanowski, R.H. / Bujnicki, J.M. / Bochtler, M. / Skowronek, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2019 Title: Crystal Structure and Directed Evolution of Specificity of NlaIV Restriction Endonuclease. Authors: Czapinska, H. / Siwek, W. / Szczepanowski, R.H. / Bujnicki, J.M. / Bochtler, M. / Skowronek, K.J. #1: Journal: Protein Eng. Des. Sel. / Year: 2005 Title: A theoretical model of restriction endonuclease NlaIV in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis and circular dichroism spectroscopy. Authors: Chmiel, A.A. / Radlinska, M. / Pawlak, S.D. / Krowarsch, D. / Bujnicki, J.M. / Skowronek, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qm2.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qm2.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 6qm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qm2_validation.pdf.gz | 409.2 KB | Display | wwPDB validaton report |
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Full document | 6qm2_full_validation.pdf.gz | 410 KB | Display | |
Data in XML | 6qm2_validation.xml.gz | 12 KB | Display | |
Data in CIF | 6qm2_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/6qm2 ftp://data.pdbj.org/pub/pdb/validation_reports/qm/6qm2 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29153.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria lactamica (bacteria) / Strain: NRCC 2118 / Gene: nlaIVR / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 References: UniProt: P50183, type II site-specific deoxyribonuclease |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-K / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 10 mg/ml of the enzyme in 15 % glycerol, 50 mM NaOH/HEPES pH 7,5, 50 mM KCl, 10 mM DTT and 5 mM CaCl2 was mixed in 1:1 ratio with double stranded DNA composed of the 5'-ATGGTACCTGC-3' and 5'- ...Details: 10 mg/ml of the enzyme in 15 % glycerol, 50 mM NaOH/HEPES pH 7,5, 50 mM KCl, 10 mM DTT and 5 mM CaCl2 was mixed in 1:1 ratio with double stranded DNA composed of the 5'-ATGGTACCTGC-3' and 5'-CAGGTACCATG-3' strands. The protein-DNA solutions were in turn mixed in 1:1 ratio with the precipitant solution containing 2 M NaCl and 100 mM citric acid, pH 5. PH range: 5 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 17, 2008 / Details: BENT MIRROR |
Radiation | Monochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 18997 / % possible obs: 98.5 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.043 / Rsym value: 0.04 / Net I/σ(I): 28.92 |
Reflection shell | Resolution: 2.8→2.97 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 1.72 / Rsym value: 0.986 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→29.72 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 11.197 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.221 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The ION IDENTITY HAS BEEN ASSIGNED TENTATIVELY.
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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: 115.889 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→29.72 Å
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