+Open data
-Basic information
Entry | Database: PDB / ID: 7z6w | |||||||||
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Title | Complex of E. coli LolA and lipoprotein | |||||||||
Components | Outer-membrane lipoprotein carrier protein | |||||||||
Keywords | TRANSPORT PROTEIN / Lipoprotein trafficking / PROTEIN TRANSPORT | |||||||||
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: 1.84 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 | 7z6w.cif.gz | 56.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z6w.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 7z6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z6w_validation.pdf.gz | 745.9 KB | Display | wwPDB validaton report |
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Full document | 7z6w_full_validation.pdf.gz | 748.8 KB | Display | |
Data in XML | 7z6w_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 7z6w_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/7z6w ftp://data.pdbj.org/pub/pdb/validation_reports/z6/7z6w | HTTPS FTP |
-Related structure data
Related structure data | 7z6xC 1ua8S S: Starting model for refinement C: citing same article (ref.) |
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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: 21529.570 Da / Num. of mol.: 1 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: 2.29 Å3/Da / Density % sol: 46.19 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, sitting drop / Details: 2.1 M DL-Malic acid pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 8, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.84→64.33 Å / Num. obs: 17042 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.037 / Rrim(I) all: 0.13 / Net I/σ(I): 14.3 / Num. measured all: 207055 / Scaling rejects: 12 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UA8 Resolution: 1.84→64.33 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.393 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.128 / 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: 91.33 Å2 / Biso mean: 29.02 Å2 / Biso min: 14.69 Å2
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Refinement step | Cycle: final / Resolution: 1.84→64.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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