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Open data
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Basic information
Entry | Database: PDB / ID: 3k1b | ||||||
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Title | Structure of OmpF porin | ||||||
![]() | Outer membrane protein F | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() colicin transmembrane transporter activity / monoatomic ion channel complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kefala, G. / Ahn, C. / Krupa, M. / Maslennikov, I. / Kwiatkowski, W. / Choe, S. / Center for Structures of Membrane Proteins (CSMP) | ||||||
![]() | ![]() Title: Structures of the OmpF porin crystallized in the presence of foscholine-12. Authors: Kefala, G. / Ahn, C. / Krupa, M. / Esquivies, L. / Maslennikov, I. / Kwiatkowski, W. / Choe, S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 263.4 KB | Display | ![]() |
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PDB format | ![]() | 214.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3k19C ![]() 2omfS C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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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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Components
#1: Protein | Mass: 37114.250 Da / Num. of mol.: 4 / Fragment: sequence database residues 1-340 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.21 Å3/Da / Density % sol: 80.19 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion / pH: 3.9 Details: 0.48 sodium phosphate monobasic, 0.72 M potassium phosphate monobasic, 0.1 M acetate pH 3.9, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2009 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 4.4→50 Å / Num. obs: 23572 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.211 / Rsym value: 0.211 / Net I/σ(I): 7.778 |
Reflection shell | Resolution: 4.4→4.48 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 3 / Num. unique all: 137454 / Rsym value: 0.512 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 2OMF Resolution: 4.39→50 Å / Cor.coef. Fo:Fc: 0.796 / Cor.coef. Fo:Fc free: 0.761 / SU B: 53.658 / SU ML: 0.668 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.011 / 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: 126.423 Å2
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Refinement step | Cycle: LAST / Resolution: 4.39→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.394→4.508 Å / Total num. of bins used: 20
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