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Yorodumi- PDB-3wju: Crystal structure of the L68D variant of mLolB from Escherichia coli -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wju | ||||||
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Title | Crystal structure of the L68D variant of mLolB from Escherichia coli | ||||||
Components | Outer-membrane lipoprotein LolB | ||||||
Keywords | TRANSPORT PROTEIN / LolA/LolB Fold | ||||||
Function / homology | Lipoprotein localisation LolA/LolB/LppX / outer membrane lipoprotein receptor (LolB), chain A / Clam / Mainly Beta / : Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Takeda, K. / Tokuda, H. / Miki, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wju.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wju.ent.gz | 35.3 KB | Display | PDB format |
PDBx/mmJSON format | 3wju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/3wju ftp://data.pdbj.org/pub/pdb/validation_reports/wj/3wju | HTTPS FTP |
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-Related structure data
Related structure data | 3wjtC 3wjvC 1iwmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: L68D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1 / Gene: lolB, ECDH1ME8569_1148 / Plasmid: pRT102 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QXY7 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 180mM ammonium sulfate, 25%(w/v) PEG8000, 20mM Tris-Hcl, 5.0%(v/v) MPD, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
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: 2.5→30 Å / Num. all: 10408 / Num. obs: 10408 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.9 % / Biso Wilson estimate: 40.1 Å2 / Rsym value: 0.054 / Net I/σ(I): 55.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.3 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: A chain of 1IWM Resolution: 2.5→25.22 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 95345.75 / 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: 41.1672 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→25.22 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: 0.074 / Total num. of bins used: 6
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Xplor file |
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