+Open data
-Basic information
Entry | Database: PDB / ID: 3re9 | ||||||
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Title | Crystal structure of sortaseC1 from Streptococcus suis | ||||||
Components | Sortase-like protein | ||||||
Keywords | TRANSFERASE / Class C sortase / sortaseC-specific lid / helix / open-form / substrate-binding site / transpeptidase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus suis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Lu, G. / Qi, J. / Gao, F. / Yan, J. / Tang, J. / Gao, G.F. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: A novel "open-form" structure of sortaseC from Streptococcus suis. Authors: Lu, G. / Qi, J. / Gao, F. / Yan, J. / Tang, J. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3re9.cif.gz | 49 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3re9.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 3re9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/3re9 ftp://data.pdbj.org/pub/pdb/validation_reports/re/3re9 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 21166.049 Da / Num. of mol.: 1 / Fragment: UNP residues 67-245 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: 05ZYH33 / Gene: SSU05_2098 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A4VY75, EC: 2.3.2.12 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCL, 0.54M sodium citrate, 8% V/V iso-propanol, 8% V/V tert-butanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.4→36.94 Å / Num. all: 7851 / Num. obs: 7831 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 11.8 | ||||||||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.77 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 6.6 / Num. unique all: 759 / Rsym value: 0.221 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→36.94 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.862 / SU B: 8.75 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R Free: 0.287 / 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: 19.091 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→36.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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