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- PDB-8g1l: Lectin domain of Aap (Staphylococcus epidermidis Accumulation Ass... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8g1l | |||||||||
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Title | Lectin domain of Aap (Staphylococcus epidermidis Accumulation Associated Protein) | |||||||||
![]() | Accumulation associated protein | |||||||||
![]() | CELL ADHESION / bacterial lectin / cell wall-attached protein / glycan binding | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Maciag, J.J. / Herr, A.B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanistic basis of staphylococcal interspecies competition for skin colonization Authors: Maciag, J.J. / Herr, A.B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169 KB | Display | ![]() |
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PDB format | ![]() | 133.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.5 KB | Display | ![]() |
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Full document | ![]() | 427.9 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8g1mC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27437.576 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: aap, SERP2398 / Plasmid: pDest-HisMBP / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 352 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PG0.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PG0.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PG0 / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 100 mM Na Acetate (pH 4.5), 22.5% BCS PEG SMEAR High (Molecular Dimensions, CalibreScientific), pentanediol and 100 mM BisTris (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 183 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→42.7658 Å / Num. obs: 121879 / % possible obs: 99.65 % / Redundancy: 8.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09085 / Rpim(I) all: 0.03388 / Rrim(I) all: 0.09719 / Net I/σ(I): 14.88 |
Reflection shell | Resolution: 1.06→1.098 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.5542 / Mean I/σ(I) obs: 4.39 / Num. unique obs: 11899 / CC1/2: 0.911 / Rpim(I) all: 0.2158 / Rrim(I) all: 0.596 / % possible all: 98.48 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.06→42.7658 Å
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Refine LS restraints |
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LS refinement shell |
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