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Open data
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Basic information
Entry | Database: PDB / ID: 3wjt | ||||||
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Title | Crystal structure of the L68D variant of mLolB | ||||||
![]() | Outer-membrane lipoprotein LolB | ||||||
![]() | TRANSPORT PROTEIN / LolA/B Fold / Outer membrane | ||||||
Function / homology | Lipoprotein localisation LolA/LolB/LppX / outer membrane lipoprotein receptor (LolB), chain A / Clam / Mainly Beta / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takeda, K. / Tokuda, H. / Miki, K. | ||||||
![]() | ![]() Title: Roles of the Protruding Loop of Factor B Essential for the Localization of Lipoproteins (LolB) in the Anchoring of Bacterial Triacylated Proteins to the Outer Membran Authors: Hayashi, Y. / Tsurumizu, R. / Tsukahara, J. / Takeda, K. / Narita, S. / Mori, M. / Miki, K. / Tokuda, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.2 KB | Display | ![]() |
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PDB format | ![]() | 38.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3wjuC ![]() 3wjvC ![]() 1iwmS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 20484.809 Da / Num. of mol.: 1 / Fragment: UNP residues 22-207 / Mutation: C1A, L68E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.42 % |
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Crystal grow | Temperature: 277 K / pH: 8 Details: 180mM ammonium sulfate, 25%(w/v) PEG8000, 20mM Tris-HCl, 5.0%(v/v) glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. obs: 24057 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 20.1 Å2 / Rsym value: 0.053 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 3.2 % / Rsym value: 0.256 / % possible all: 72.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: A CHAIN OF 1IWM Resolution: 1.55→28.17 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 133040.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.4798 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→28.17 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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