+Open data
-Basic information
Entry | Database: PDB / ID: 7z6x | |||||||||
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Title | Complex of E. coli LolA R43L mutant and lipoprotein | |||||||||
Components | Outer-membrane lipoprotein carrier protein | |||||||||
Keywords | TRANSPORT PROTEIN / Lipoprotein trafficking / periplasmic chaperone | |||||||||
Function / homology | Outer membrane lipoprotein carrier protein LolA, Proteobacteria / Outer membrane lipoprotein carrier protein LolA / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein localisation LolA/LolB/LppX / lipoprotein localization to outer membrane / lipoprotein transport / outer membrane-bounded periplasmic space / Chem-IG7 / Outer-membrane lipoprotein carrier protein Function and homology information | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | |||||||||
Authors | Kaplan, E. / Greene, N.P. / Koronakis, V. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Structural basis of lipoprotein recognition by the bacterial Lol trafficking chaperone LolA. Authors: Kaplan, E. / Greene, N.P. / Jepson, A.E. / Koronakis, V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z6x.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z6x.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 7z6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/7z6x ftp://data.pdbj.org/pub/pdb/validation_reports/z6/7z6x | HTTPS FTP |
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-Related structure data
Related structure data | 7z6wC 2zpdS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21485.535 Da / Num. of mol.: 1 / Mutation: R43L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: lolA, lplA, yzzV, b0891, JW0874 / Production host: Escherichia coli (E. coli) / References: UniProt: P61316 |
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#2: Chemical | ChemComp-IG7 / [( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.55 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, sitting drop / Details: 50 mM bis-Tris pH 6.0, 30% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.06→63.26 Å / Num. obs: 11241 / % possible obs: 98.2 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.036 / Rrim(I) all: 0.092 / Net I/σ(I): 10.3 / Num. measured all: 70351 / Scaling rejects: 22 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZPD Resolution: 2.06→38.27 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.746 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.19 Å2 / Biso mean: 50.648 Å2 / Biso min: 31.59 Å2
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Refinement step | Cycle: final / Resolution: 2.06→38.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.063→2.116 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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