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Open data
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Basic information
Entry | Database: PDB / ID: 3gp6 | ||||||
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Title | Crystal structure of PagP in SDS/MPD | ||||||
![]() | Protein pagP | ||||||
![]() | TRANSFERASE / PALMITOYLTRANSFERASE / BETA-BARREL / OUTER MEMBRANE ENZYME / PagP / SDS / MPD | ||||||
Function / homology | ![]() lipid IVA palmitoyltransferase / O-palmitoyltransferase activity / lipid A biosynthetic process / cell outer membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cuesta-Seijo, J.A. / Prive, G.G. | ||||||
![]() | ![]() Title: PagP crystallized from SDS/cosolvent reveals the route for phospholipid access to the hydrocarbon ruler. Authors: Cuesta-Seijo, J.A. / Neale, C. / Khan, M.A. / Moktar, J. / Tran, C.D. / Bishop, R.E. / Pomes, R. / Prive, G.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.7 KB | Display | ![]() |
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PDB format | ![]() | 71.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1thqS 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19240.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 80 molecules ![](data/chem/img/SDS.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/LI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/LI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SDS / #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-MRD / ( | #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1M MPD, 0.1M citrate pH 5.6, 1.7M lithium sulphate, 0.3M ammonium sulphate, SDS, Phase separation, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. all: 40433 / Num. obs: 40433 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.068 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.36 / Num. unique all: 1633 / Rsym value: 0.531 / % possible all: 80.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1THQ Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.009 / SU ML: 0.05 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / ESU R: 0.062 / ESU R Free: 0.06 / Stereochemistry target values: Refmac 5 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The author states that the crystallization conditions included large amounts of lithium, but it cannot be confirmed that the ion is lithium ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The author states that the crystallization conditions included large amounts of lithium, but it cannot be confirmed that the ion is lithium based on electron density.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.065 Å2
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Refine analyze | Luzzati coordinate error obs: 0.202 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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