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Yorodumi- PDB-8q2p: Structure of the membrane integral lipoprotein N-acyltransferase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q2p | |||||||||
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Title | Structure of the membrane integral lipoprotein N-acyltransferase Lnt from E. coli by using Se-MAG for the the lipid cubic phase crystallization | |||||||||
Components | Apolipoprotein N-acyltransferase | |||||||||
Keywords | TRANSFERASE / co-crystallization / experimental phasing / lipoprotein N-acyltransferase / selenium-sulfur hydrogen bond / seleno-monoacylglyceride / X-ray scattering | |||||||||
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 K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | |||||||||
Authors | Huang, C.-Y. / Boland, C. / Kaki, S.S. / Wang, M. / Olieric, V. / Caffrey, M. | |||||||||
Funding support | European Union, Ireland, 2items
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Citation | Journal: Crystals / Year: 2023 Title: Se-MAG Is a Convenient Additive for Experimental Phasing and Structure Determination of Membrane Proteins Crystallised by the Lipid Cubic Phase (In Meso) Method Authors: Boland, C. / Huang, C.Y. / Shanker Kaki, S. / Wang, M. / Olieric, V. / Caffrey, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q2p.cif.gz | 164 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q2p.ent.gz | 105.6 KB | Display | PDB format |
PDBx/mmJSON format | 8q2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/8q2p ftp://data.pdbj.org/pub/pdb/validation_reports/q2/8q2p | HTTPS FTP |
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-Related structure data
Related structure data | 8q2oC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 56823.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lnt, cutE, b0657, JW0654 / Production host: Escherichia coli (E. coli) References: UniProt: P23930, apolipoprotein N-acyltransferase |
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-Non-polymers , 5 types, 328 molecules
#2: Chemical | ChemComp-IRY / [( Mass: 381.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C17H34O4Se / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-OLC / ( #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PG5 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.78 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6 Details: 0.1 M MES-NaOH pH 6.0, 8 %(v/v) MPD, and 0.4 M sodium or potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97939 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97939 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→43.02 Å / Num. obs: 87726 / % possible obs: 99 % / Redundancy: 80.88 % / Biso Wilson estimate: 27.21 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.31 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.28 % / Mean I/σ(I) obs: 0.88 / Num. unique obs: 6484 / CC1/2: 0.99 / Rrim(I) all: 2.95 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→43.02 Å / SU ML: 0.2201 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2948 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: 31.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→43.02 Å
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Refine LS restraints |
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LS refinement shell |
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