+Open data
-Basic information
Entry | Database: PDB / ID: 5o77 | ||||||
---|---|---|---|---|---|---|---|
Title | Klebsiella pneumoniae OmpK35 | ||||||
Components | OmpK35 | ||||||
Keywords | MEMBRANE PROTEIN / Outer membrane protein / porin / ion transport / OmpF ortholog | ||||||
Function / homology | Function and homology information porin activity / monoatomic ion transmembrane transport / cell outer membrane Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | van den berg, B. / Pathania, M. / Zahn, M. | ||||||
Citation | Journal: Acs Infect Dis. / Year: 2018 Title: Getting Drugs into Gram-Negative Bacteria: Rational Rules for Permeation through General Porins. Authors: Acosta-Gutierrez, S. / Ferrara, L. / Pathania, M. / Masi, M. / Wang, J. / Bodrenko, I. / Zahn, M. / Winterhalter, M. / Stavenger, R.A. / Pages, J.M. / Naismith, J.H. / van den Berg, B. / ...Authors: Acosta-Gutierrez, S. / Ferrara, L. / Pathania, M. / Masi, M. / Wang, J. / Bodrenko, I. / Zahn, M. / Winterhalter, M. / Stavenger, R.A. / Pages, J.M. / Naismith, J.H. / van den Berg, B. / Page, M.G.P. / Ceccarelli, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5o77.cif.gz | 151 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5o77.ent.gz | 118.2 KB | Display | PDB format |
PDBx/mmJSON format | 5o77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o77_validation.pdf.gz | 954.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5o77_full_validation.pdf.gz | 959.5 KB | Display | |
Data in XML | 5o77_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 5o77_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/5o77 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/5o77 | HTTPS FTP |
-Related structure data
Related structure data | 5o79C 6eneC 4gcpS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 37322.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: pBAD24 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Omp8 / References: UniProt: A0A1P8FCM7 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 13% PEG 2000MME, 0.1 M calcium chloride, 0.1 M Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→43.41 Å / Num. obs: 61689 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rpim(I) all: 0.044 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2 / Rpim(I) all: 5.21 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GCP Resolution: 1.5→43.41 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.456 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.063 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.891 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.5→43.41 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|