+Open data
-Basic information
Entry | Database: PDB / ID: 5dwc | ||||||
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Title | Crystal structure of restriction endonuclease AgeI | ||||||
Components | Type-2 restriction enzyme AgeI | ||||||
Keywords | HYDROLASE / restriction endonuclease / PD-(D/E)XK nuclease | ||||||
Function / homology | BsaWI restriction endonuclease type 2 / BsaWI restriction endonuclease type 2 / type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / Type II restriction enzyme AgeI Function and homology information | ||||||
Biological species | Thalassobius gelatinovorus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Tamulaitiene, G. / Ramonaite, I. / Grazulis, S. / Siksnys, V. | ||||||
Funding support | Lithuania, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA. Authors: Tamulaitiene, G. / Jovaisaite, V. / Tamulaitis, G. / Songailiene, I. / Manakova, E. / Zaremba, M. / Grazulis, S. / Xu, S.Y. / Siksnys, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dwc.cif.gz | 119.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dwc.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 5dwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dwc_validation.pdf.gz | 421.7 KB | Display | wwPDB validaton report |
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Full document | 5dwc_full_validation.pdf.gz | 422 KB | Display | |
Data in XML | 5dwc_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 5dwc_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/5dwc ftp://data.pdbj.org/pub/pdb/validation_reports/dw/5dwc | HTTPS FTP |
-Related structure data
Related structure data | 5dwaC 5dwbSC 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: 30593.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thalassobius gelatinovorus (bacteria) / Gene: ageIR / Plasmid: pRRS-AgeIRM / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 References: UniProt: Q9KHV6, type II site-specific deoxyribonuclease |
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#2: 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: 2.18 Å3/Da / Density % sol: 43.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Crystallization buffer was 0.1 M NaCl, 0.1 M Na-Hepes (pH 7.5), 22% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.91 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2014 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→33.329 Å / Num. all: 9795 / Num. obs: 9795 / % possible obs: 100 % / Redundancy: 5.8 % / Biso Wilson estimate: 31.5 Å2 / Rpim(I) all: 0.057 / Rrim(I) all: 0.141 / Rsym value: 0.118 / Net I/av σ(I): 5.859 / Net I/σ(I): 12.5 / Num. measured all: 56770 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DWB Resolution: 2.5→33.329 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.74 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.25 Å2 / Biso mean: 36.9635 Å2 / Biso min: 4.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→33.329 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 5.2321 Å / Origin y: 0.3455 Å / Origin z: 15.8391 Å
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Refinement TLS group | Selection details: chain A |