+Open data
-Basic information
Entry | Database: PDB / ID: 4o5j | ||||||
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Title | Crystal structure of SabA from Helicobacter pylori | ||||||
Components | Uncharacterized protein | ||||||
Keywords | 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 / : Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Pang, S.S. / Nguyen, S.T.S. / Whisstock, J.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o5j.cif.gz | 163.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o5j.ent.gz | 135 KB | Display | PDB format |
PDBx/mmJSON format | 4o5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/4o5j ftp://data.pdbj.org/pub/pdb/validation_reports/o5/4o5j | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: C694_03730, SabA / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: K4NCD9, UniProt: A0A2I8VBX7*PLUS | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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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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Diffraction source |
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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
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→90.02 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 5.433 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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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