+Open data
-Basic information
Entry | Database: PDB / ID: 6gw5 | ||||||
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Title | X-ray structure of the Helicobacter pylori SabA adhesin domain | ||||||
Components | Putative Outer membrane protein | ||||||
Keywords | CELL ADHESION / Helicobacter pylori / adhesin / outer membrane protein / Lewis X / lectin | ||||||
Function / homology | Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Putative Outer membrane protein Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | ||||||
Authors | Coppens, F. / Remaut, H. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Mol. Microbiol. / Year: 2018 Title: Hop-family Helicobacter outer membrane adhesins form a novel class of Type 5-like secretion proteins with an interrupted beta-barrel domain. Authors: Coppens, F. / Castaldo, G. / Debraekeleer, A. / Subedi, S. / Moonens, K. / Lo, A. / Remaut, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gw5.cif.gz | 166.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gw5.ent.gz | 130 KB | Display | PDB format |
PDBx/mmJSON format | 6gw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gw5_validation.pdf.gz | 439.2 KB | Display | wwPDB validaton report |
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Full document | 6gw5_full_validation.pdf.gz | 446.3 KB | Display | |
Data in XML | 6gw5_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 6gw5_validation.cif.gz | 40.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/6gw5 ftp://data.pdbj.org/pub/pdb/validation_reports/gw/6gw5 | HTTPS FTP |
-Related structure data
Related structure data | 4o5jS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 23 - 438 / Label seq-ID: 2 - 417
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-Components
#1: Protein | Mass: 48668.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: jhp_0662 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9ZLB8 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 15% PEG 3350, 0.2 M KF, 0.1 M citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→47.5 Å / Num. obs: 140735 / % possible obs: 97 % / Redundancy: 4 % / Biso Wilson estimate: 45.2 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.119 / Net I/av σ(I): 11.78 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.52→2.59 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 10599 / CC1/2: 0.79 / Rrim(I) all: 0.897 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O5J Resolution: 2.52→47.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.489 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.473 / ESU R Free: 0.29 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.51 Å2
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Refinement step | Cycle: 1 / Resolution: 2.52→47.5 Å
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Refine LS restraints |
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