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- PDB-8t1y: Crystal Structure of Porphyromonas gingivalis Sialidase (PG_0352)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8t1y | ||||||
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Title | Crystal Structure of Porphyromonas gingivalis Sialidase (PG_0352) Bound to Neu5Ac2en (DANA) | ||||||
![]() | Sialidase | ||||||
![]() | HYDROLASE / sialidase / neuraminidase / carbohydrate binding / virulence factor | ||||||
Function / homology | ![]() exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / intracellular membrane-bounded organelle / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Clark, N.D. / Malkowski, M.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Functional and structural analyses reveal that a dual domain sialidase protects bacteria from complement killing through desialylation of complement factors. Authors: Clark, N.D. / Pham, C. / Kurniyati, K. / Sze, C.W. / Coleman, L. / Fu, Q. / Zhang, S. / Malkowski, M.G. / Li, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 253.5 KB | Display | ![]() |
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PDB format | ![]() | 167.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 830.1 KB | Display | ![]() |
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Full document | ![]() | 832.2 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8febSC ![]() 8t1zC ![]() 8t24C ![]() 8t26C ![]() 8t27C S: Starting model for refinement 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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1 |
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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/DAN.gif)
![](data/chem/img/DAN.gif)
#1: Protein | Mass: 56538.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Sugar | ChemComp-DAN / |
-Non-polymers , 4 types, 246 molecules ![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PG4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.48 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.7 M ammonium citrate tribasic, pH 7.0 |
-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: Nov 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→44 Å / Num. obs: 37392 / % possible obs: 98.76 % / Redundancy: 3.9 % / Biso Wilson estimate: 36.56 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1458 / Rpim(I) all: 0.085 / Rrim(I) all: 0.1692 / Net I/σ(I): 7.33 |
Reflection shell | Resolution: 2.14→2.217 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.904 / Num. unique obs: 3718 / CC1/2: 0.752 / CC star: 0.927 / Rpim(I) all: 0.5112 / Rrim(I) all: 1.042 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8FEB Resolution: 2.14→44 Å / SU ML: 0.2936 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3684 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→44 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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