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- PDB-3fn6: Crystal structure of sortase A from Streptococcus pyogenes seroty... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fn6 | ||||||
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Title | Crystal structure of sortase A from Streptococcus pyogenes serotype M1 strain SF370 with the active site Cys in its sulphenic acid form | ||||||
![]() | Sortase A | ||||||
![]() | HYDROLASE / sortase-fold | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Banfield, M.J. | ||||||
![]() | ![]() Title: Crystal Structure of Streptococcus pyogenes Sortase A: Implications for Sortase mechanism Authors: Race, P.R. / Bentley, M.L. / Melvin, J.A. / Crow, A. / Hughes, R.K. / Smith, W.D. / Sessions, R.B. / Kehoe, M.A. / McCafferty, D.G. / Banfield, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.4 KB | Display | ![]() |
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PDB format | ![]() | 35.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3fn5C ![]() 3fn7C ![]() 1t2pS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 20496.186 Da / Num. of mol.: 1 / Fragment: Catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: serotype M1 strian SF370 / Gene: M5005_Spy0875, Spy1154, SPy_1154 / Plasmid: pET28a / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM Tris (pH 6 - 7), 20 30 % (w/v) polyethyleneglycol (PEG) 8000 and 200 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 1, 2007 |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→26.26 Å / Num. all: 15111 / Num. obs: 15111 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.064 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 2170 / Rsym value: 0.258 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1T2P Resolution: 1.9→26.26 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.125 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.142 / 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: 17.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→26.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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