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- PDB-6oyc: Glycosylation Associate Protein (Gap123) complex from Streptococc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6oyc | ||||||
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Title | Glycosylation Associate Protein (Gap123) complex from Streptococcus agalactiae | ||||||
![]() | (Glycosylation Associate Protein ...) x 3 | ||||||
![]() | SUGAR BINDING PROTEIN / Glycosylation / Secretion / lectin | ||||||
Function / homology | ![]() | ||||||
Biological species | Streptococcus agalactiae serotype V | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | zhang, H. / Wu, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Glycosylation Associate Protein (Gap123) complex from Streptococcus agalactiae Authors: zhang, H. / Zhu, F. / Wu, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 289.7 KB | Display | ![]() |
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PDB format | ![]() | 230.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 280.5 KB | Display | ![]() |
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Full document | ![]() | 281.8 KB | Display | |
Data in XML | ![]() | 2 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6e2i 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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3 | ![]()
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4 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Glycosylation Associate Protein ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 60541.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-611 / 2603 V/R / Gene: SAG1452 / Production host: ![]() ![]() |
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#2: Protein | Mass: 59251.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-611 / 2603 V/R / Gene: SAG1451 / Production host: ![]() ![]() |
#3: Protein | Mass: 37928.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-611 / 2603 V/R / Gene: SAG1450 / Production host: ![]() ![]() |
-Non-polymers , 3 types, 419 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5, 5% PEG 400, 2M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→49.272 Å / Num. obs: 72701 / % possible obs: 99.55 % / Redundancy: 14.1 % / Net I/σ(I): 28.13 |
Reflection shell | Resolution: 2.35→2.43 Å / Num. unique obs: 7084 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6E2I ![]() 6e2i Resolution: 2.351→49.272 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.21
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.351→49.272 Å
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Refine LS restraints |
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LS refinement shell |
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