+Open data
-Basic information
Entry | Database: PDB / ID: 2xgr | ||||||
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Title | extracellular endonuclease | ||||||
Components | SPD1 NUCLEASE | ||||||
Keywords | HYDROLASE / METAL BINDING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOCOCCUS PYOGENES SEROTYPE M1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å | ||||||
Authors | Korczynska, J.E. / Turkenburg, J.P. / Taylor, E.J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: The Structural Characterization of a Prophage-Encoded Extracellular DNase from Streptococcus Pyogenes. Authors: Korczynska, J.E. / Turkenburg, J.P. / Taylor, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xgr.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xgr.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xgr_validation.pdf.gz | 446.3 KB | Display | wwPDB validaton report |
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Full document | 2xgr_full_validation.pdf.gz | 450.3 KB | Display | |
Data in XML | 2xgr_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 2xgr_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/2xgr ftp://data.pdbj.org/pub/pdb/validation_reports/xg/2xgr | HTTPS FTP |
-Related 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: 28400.756 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PYOGENES SEROTYPE M1 (bacteria) Strain: GAS-SF370 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIPL / References: UniProt: Q9A0M1, deoxyribonuclease I | ||
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#2: Chemical | ChemComp-PEG / #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: 2.62 Å3/Da / Density % sol: 52.72 % / Description: NONE |
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Crystal grow | pH: 6 / Details: MALIC/MES/TRIS SYSTEM PH 6.0 25% PEG 1.5K. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.934 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→51.1 Å / Num. obs: 30345 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 1.7→38.21 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.686 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES FROM 1-32, 94-114 AND 251-252 ARE DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.341 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→38.21 Å
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Refine LS restraints |
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