+Open data
-Basic information
Entry | Database: PDB / ID: 2fu2 | ||||||
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Title | Crystal structure of protein SPy2152 from Streptococcus pyogenes | ||||||
Components | Hypothetical protein SPy2152 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Ta0600-like / Ta0600-like superfamily / Enterocin A Immunity / bacteriocin immunity / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha / Bacteriocin / Bacteriocin Function and homology information | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Chang, C. / Cymborowski, M. / Otwinowski, Z. / Minor, W. / Lezondra, L.-E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2009 Title: The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes. Authors: Chang, C. / Coggill, P. / Bateman, A. / Finn, R.D. / Cymborowski, M. / Otwinowski, Z. / Minor, W. / Volkart, L. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fu2.cif.gz | 26.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fu2.ent.gz | 19.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fu2_validation.pdf.gz | 421.8 KB | Display | wwPDB validaton report |
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Full document | 2fu2_full_validation.pdf.gz | 422.1 KB | Display | |
Data in XML | 2fu2_validation.xml.gz | 6 KB | Display | |
Data in CIF | 2fu2_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/2fu2 ftp://data.pdbj.org/pub/pdb/validation_reports/fu/2fu2 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11468.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Derivatives / References: UniProt: Q99XL4, UniProt: Q48QT2*PLUS |
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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: 1.65 Å3/Da / Density % sol: 25.63 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 20 % PEG 8000, Mes pH 6.0, Ca(OAc)2 , VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97907 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2005 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→50 Å / Num. all: 5139 / Num. obs: 4682 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 30.26 |
Reflection shell | Resolution: 2.01→2.03 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 3.62 / Num. unique all: 75 / % possible all: 58.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→34.94 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.909 / SU B: 12.189 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.279 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 35.876 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→34.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.207 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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