+Open data
-Basic information
Entry | Database: PDB / ID: 3hp7 | ||||||
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Title | Putative hemolysin from Streptococcus thermophilus. | ||||||
Components | Hemolysin, putative | ||||||
Keywords | structural genomics / unknown function / APC64019 / hemolysin / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.53 Å | ||||||
Authors | Osipiuk, J. / Hatzos, C. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: X-ray crystal structure of putative hemolysin from Streptococcus thermophilus. Authors: Osipiuk, J. / Hatzos, C. / Cobb, G. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hp7.cif.gz | 138.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hp7.ent.gz | 114.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hp7_validation.pdf.gz | 438.6 KB | Display | wwPDB validaton report |
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Full document | 3hp7_full_validation.pdf.gz | 441 KB | Display | |
Data in XML | 3hp7_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 3hp7_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/3hp7 ftp://data.pdbj.org/pub/pdb/validation_reports/hp/3hp7 | 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: 32424.104 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Strain: LMG 18311 / Gene: stu1215 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5M3Z4 |
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#2: Chemical | ChemComp-EOH / |
#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: 2.71 Å3/Da / Density % sol: 54.55 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris buffer, 20% ethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 29, 2009 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→36.4 Å / Num. all: 54173 / Num. obs: 54173 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.067 / Χ2: 2.192 / Net I/σ(I): 55.624 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 2.07 / Num. unique all: 2688 / Χ2: 0.939 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.53→36.4 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.965 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 59.76 Å2 / Biso mean: 23.675 Å2 / Biso min: 9.28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→36.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.527→1.567 Å / Total num. of bins used: 20
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