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- PDB-4gcs: Crystal Structure of E. coli OmpF porin in complex with Ertapenem -
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Open data
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Basic information
Entry | Database: PDB / ID: 4gcs | ||||||
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Title | Crystal Structure of E. coli OmpF porin in complex with Ertapenem | ||||||
![]() | Outer membrane protein F | ||||||
![]() | MEMBRANE PROTEIN/ANTIBIOTIC / Beta-barrel / Protein-drug complex / Trimer / Non-specific channel / Ertapenem binding / Outer membrane / MEMBRANE PROTEIN-ANTIBIOTIC complex | ||||||
Function / homology | ![]() colicin transmembrane transporter activity / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / protein transport ...colicin transmembrane transporter activity / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / protein transport / monoatomic ion transmembrane transport / lipid binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ziervogel, B.K. / Roux, B. | ||||||
![]() | ![]() Title: The Binding of Antibiotics in OmpF Porin. Authors: Ziervogel, B.K. / Roux, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.9 KB | Display | ![]() |
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PDB format | ![]() | 117.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 31.9 KB | Display | |
Data in CIF | ![]() | 45.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 1 / Auth seq-ID: 8 - 340 / Label seq-ID: 9 - 341
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Components
#1: Protein | Mass: 37171.301 Da / Num. of mol.: 2 / Fragment: UNP Residues 23-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50% PEG 200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2011 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→50 Å / Num. all: 65981 / Num. obs: 64277 / % possible obs: 97.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 5.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.589 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→36.53 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2548 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.87→1.918 Å / Total num. of bins used: 20
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