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Open data
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Basic information
Entry | Database: PDB / ID: 3pgs | ||||||
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Title | Phe3Gly mutant of EcFadL | ||||||
![]() | Long-chain fatty acid transport protein | ||||||
![]() | LIPID TRANSPORT / beta barrel outer membrane / outer membrane | ||||||
Function / homology | ![]() long-chain fatty acid transporting porin activity / ligand-gated channel activity / cell outer membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van den Berg, B. / Lepore, B.W. | ||||||
![]() | ![]() Title: From the Cover: Ligand-gated diffusion across the bacterial outer membrane. Authors: Lepore, B.W. / Indic, M. / Pham, H. / Hearn, E.M. / Patel, D.R. / van den Berg, B. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 374.7 KB | Display | ![]() |
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PDB format | ![]() | 307.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 45 KB | Display | |
Data in CIF | ![]() | 64.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2r89C ![]() 2r8aC ![]() 3pf1C ![]() 3pgrC ![]() 3pguC ![]() 1t16S S: Starting model for refinement C: citing same article ( |
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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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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46676.871 Da / Num. of mol.: 2 / Fragment: Mature form (UNP Residues 26-446) / Mutation: F28G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 803 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/C8E.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/2PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/C8E.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/2PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / | ||||||||
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#3: Chemical | ChemComp-C8E / ( #4: Chemical | ChemComp-LDA / #5: Chemical | #6: Chemical | ChemComp-2PE / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.33 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M NaOAc pH 5.5, 8.8 w/v PEG 2000 MME. Protein dialyzed in Tris buffer, C8E4 prior to setup, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2010 / Details: OXFORD DANFYSIK TOROIDAL |
Radiation | Monochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8486→39 Å / Num. all: 119844 / Num. obs: 119844 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 1.8486→1.88 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.818 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1T16 Resolution: 1.9→38.778 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 18.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.929 Å2 / ksol: 0.357 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→38.778 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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