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Open data
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Basic information
Entry | Database: PDB / ID: 3wjv | ||||||
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Title | Crystal structure of the L68E variant of mLolB | ||||||
![]() | Outer-membrane lipoprotein LolB | ||||||
![]() | TRANSPORT PROTEIN / LolA/LolB 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 | ![]() | 50.5 KB | Display | ![]() |
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PDB format | ![]() | 35 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.6 KB | Display | ![]() |
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Full document | ![]() | 450.1 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wjtC ![]() 3wjuC ![]() 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
#1: Protein | Mass: 21241.678 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: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 180mM ammonium sulfate, 25%(w/v) PEG8000, 15%(v/v) glycerol, 20mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-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: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 7140 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 30.5 Å2 / Rsym value: 0.07 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 640 / Rsym value: 0.23 / % possible all: 85.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: A chain of 1IWM Resolution: 2.4→29.16 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 63406.8 / 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: 59.3137 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→29.16 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
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Xplor file |
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