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Open data
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Basic information
Entry | Database: PDB / ID: 2zld | ||||||
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Title | Structure of OmpF co-crystallized with T83 | ||||||
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![]() | MEMBRANE PROTEIN / BtuB / colicin E3 / ribosomal RNAase / disordered T83 / Tol system / Ion transport / Membrane / Outer membrane / Phage recognition / Porin / Transmembrane / Transport | ||||||
Function / homology | ![]() colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport ...colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport / monoatomic ion channel activity / lipid binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cramer, W.A. / Zakharov, S.D. / Yamashita, E. | ||||||
![]() | ![]() Title: Crystal structures of the OmpF porin: function in a colicin translocon. Authors: Yamashita, E. / Zhalnina, M.V. / Zakharov, S.D. / Sharma, O. / Cramer, W.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137 KB | Display | ![]() |
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PDB format | ![]() | 108.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 410.5 KB | Display | ![]() |
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Full document | ![]() | 413.8 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zfgC ![]() 2omfS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 1 / Auth seq-ID: 1 - 340 / Label seq-ID: 1 - 340
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Components
#1: Protein | Mass: 37114.250 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 613.749 Da / Num. of mol.: 2 / Fragment: T83 (RESIDUES 1-83) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() Sequence details | THE AUTHOR CO-CRYSTALLIZED THE OMPF WITH THE N-TERMINAL TRANSLOCATION DOMAIN OF COLICIN E3 (T83). ...THE AUTHOR CO-CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.82 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Highest resolution: 3 Å / Num. obs: 17885 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.076 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OMF Resolution: 3→101.02 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.857 / SU B: 23.547 / SU ML: 0.438 / Cross valid method: THROUGHOUT / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.67 Å2
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Refinement step | Cycle: LAST / Resolution: 3→101.02 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: 2619 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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