+Open data
-Basic information
Entry | Database: PDB / ID: 2xh3 | ||||||
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Title | extracellular nuclease | ||||||
Components | SPD1 NUCLEASE | ||||||
Keywords | HYDROLASE / ENDONUCLEASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOCOCCUS PYOGENES SEROTYPE M1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.49 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 | 2xh3.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xh3.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 2xh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xh3_validation.pdf.gz | 450.2 KB | Display | wwPDB validaton report |
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Full document | 2xh3_full_validation.pdf.gz | 456.4 KB | Display | |
Data in XML | 2xh3_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 2xh3_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/2xh3 ftp://data.pdbj.org/pub/pdb/validation_reports/xh/2xh3 | HTTPS FTP |
-Related structure data
Related structure data | 2xgrSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28357.732 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PYOGENES SEROTYPE M1 (bacteria) Strain: GAS-SF370 / Plasmid: PET28LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIPL / References: UniProt: Q9A0M1, deoxyribonuclease I #2: Chemical | ChemComp-PEG / | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.57 Å3/Da / Density % sol: 52.2 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.2M NA CITRATE, 0.1M BIS-TRIS PROPANE PH 8.5, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 5, 2010 / Details: OSMIC MULTILAYER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50.9 Å / Num. obs: 18955 / % possible obs: 90.3 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.48→2.61 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.5 / % possible all: 82.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XGR Resolution: 2.49→113.55 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.897 / SU B: 6.637 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-47, 87-112 ARE DISORDERED
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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: 38.523 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→113.55 Å
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Refine LS restraints |
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