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Yorodumi- PDB-8rqr: In meso structure of apolipoprotein N-acyltransferase, Lnt, from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rqr | |||||||||||||||
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Title | In meso structure of apolipoprotein N-acyltransferase, Lnt, from Escherichia coli in 7.10 monoacylglycerol | |||||||||||||||
Components | Apolipoprotein N-acyltransferase | |||||||||||||||
Keywords | MEMBRANE PROTEIN / N-acyltransferase | |||||||||||||||
Function / homology | Function and homology information apolipoprotein N-acyltransferase / N-acyltransferase activity / lipoprotein biosynthetic process / outer membrane-bounded periplasmic space / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | |||||||||||||||
Authors | Smithers, L. / Boland, C. / Krawinski, P. / Caffrey, M. | |||||||||||||||
Funding support | Ireland, 4items
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Citation | Journal: Cryst.Growth Des. / Year: 2024 Title: 7.10 MAG. A Novel Host Monoacylglyceride for In Meso (Lipid Cubic Phase) Crystallization of Membrane Proteins. Authors: Krawinski, P. / Smithers, L. / van Dalsen, L. / Boland, C. / Ostrovitsa, N. / Perez, J. / Caffrey, M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rqr.cif.gz | 380.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rqr.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8rqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rqr_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8rqr_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8rqr_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 8rqr_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/8rqr ftp://data.pdbj.org/pub/pdb/validation_reports/rq/8rqr | HTTPS FTP |
-Related structure data
Related structure data | 8rqpC 8rqqC 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: 59280.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lnt, cutE, b0657, JW0654 / Production host: Escherichia coli (E. coli) References: UniProt: P23930, apolipoprotein N-acyltransferase | ||||||
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#2: Chemical | ChemComp-A1H2K / Mass: 342.513 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H38O4 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-GOL / #4: 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: 2.47 Å3/Da / Density % sol: 50.11 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100 mM MES pH 6.0, 8 %(v/v) MPD, and 50-400 mM sodium or potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Dec 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→46.5 Å / Num. obs: 30881 / % possible obs: 99.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 33.28 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.19→2.27 Å / Num. unique obs: 2997 / CC1/2: 0.31 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→46.5 Å / SU ML: 0.2809 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.771 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→46.5 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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