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Open data
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Basic information
Entry | Database: PDB / ID: 4o5j | ||||||
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Title | Crystal structure of SabA from Helicobacter pylori | ||||||
![]() | Uncharacterized protein | ||||||
![]() | CELL ADHESION / tetratricopeptide repeat / Adhesin / Carbohydrate/Sugar Binding / outer membrane protein / Helicobacter pylori | ||||||
Function / homology | SabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Outer membrane protein / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pang, S.S. / Nguyen, S.T.S. / Whisstock, J.C. | ||||||
![]() | ![]() Title: The three-dimensional structure of the extracellular adhesion domain of the sialic acid-binding adhesin SabA from Helicobacter pylori Authors: Pang, S.S. / Nguyen, S.T.S. / Perry, A.J. / Day, C.J. / Panjikar, S. / Tiralongo, J. / Whisstock, J.C. / Kwok, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.1 KB | Display | ![]() |
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PDB format | ![]() | 135 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.3 KB | Display | ![]() |
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Full document | ![]() | 453.7 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 23.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 50298.727 Da / Num. of mol.: 1 Fragment: N-terminal extracellular adhesion domain, UNP residues 4-463 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6 Å3/Da / Density % sol: 79.49 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 200mM sodium acetate, 18-20% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.2→90.03 Å / Num. all: 60972 / Num. obs: 60966 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.3 % / Biso Wilson estimate: 36.6 Å2 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1,2
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALL
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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: 57.126 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→90.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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