+Open data
-Basic information
Entry | Database: PDB / ID: 5ldv | ||||||
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Title | Crystal Structures of MOMP from Campylobacter jejuni | ||||||
Components | MOMP porin | ||||||
Keywords | MEMBRANE PROTEIN / Porin | ||||||
Function / homology | Campylobacter major outer membrane / Campylobacter major outer membrane protein / metal ion binding / N-OCTANE / MOMP porin Function and homology information | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wallat, G.D. / Ferrara, L.M.G. / Moynie, L. / Naismith, J.H. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2016 Title: MOMP from Campylobacter jejuni Is a Trimer of 18-Stranded beta-Barrel Monomers with a Ca(2+) Ion Bound at the Constriction Zone. Authors: Ferrara, L.G. / Wallat, G.D. / Moynie, L. / Dhanasekar, N.N. / Aliouane, S. / Acosta-Gutierrez, S. / Pages, J.M. / Bolla, J.M. / Winterhalter, M. / Ceccarelli, M. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ldv.cif.gz | 172.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ldv.ent.gz | 136.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ldv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ldv_validation.pdf.gz | 443.7 KB | Display | wwPDB validaton report |
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Full document | 5ldv_full_validation.pdf.gz | 445.2 KB | Display | |
Data in XML | 5ldv_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 5ldv_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/5ldv ftp://data.pdbj.org/pub/pdb/validation_reports/ld/5ldv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44146.195 Da / Num. of mol.: 1 / Mutation: T1G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: momp / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q659I5 | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | ChemComp-1PE / | ||
#4: Chemical | ChemComp-OCT / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.09 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 4.25 Details: 0.05M sodium citrate, 35% (v/v) Peg 400, 0.07 M potassium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.06733 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06733 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→39.24 Å / Num. obs: 28313 / % possible obs: 99.5 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.89 |
Reflection shell | Resolution: 2.1→2.175 Å |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39.24 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.587 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.166 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.064 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→39.24 Å
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Refine LS restraints |
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