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- PDB-7aci: In meso structure of apolipoprotein N-acyltransferase, Lnt, from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7aci | ||||||
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Title | In meso structure of apolipoprotein N-acyltransferase, Lnt, from Escherichia coli in 9.8 monoacylglycerol | ||||||
![]() | Apolipoprotein N-acyltransferase | ||||||
![]() | MEMBRANE PROTEIN / Nitrilase fold / helical bundle | ||||||
Function / homology | ![]() apolipoprotein N-acyltransferase / N-acyltransferase activity / lipoprotein biosynthetic process / outer membrane-bounded periplasmic space / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Smithers, L. / van Dalsen, L. / Boland, C. / Caffrey, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: 9.8 MAG. A new host lipid for in meso (lipid cubic phase) crystallization of integral membrane proteins Authors: van Dalsen, L. / Smithers, L. / Boland, C. / Weichert, D. / Caffrey, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 366.9 KB | Display | ![]() |
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PDB format | ![]() | 251.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7acgC ![]() 5n6hS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Gene: lnt, ACU57_00505, AM464_20560, AUQ13_21565, BMA87_17500, BUE81_17200, BvCms2454_02009, BvCmsHHP001_00880, BvCmsKSNP120_02778, BvCmsKSP076_04015, BW690_14780, C5N07_14455, C9Z39_12310, CA593_ ...Gene: lnt, ACU57_00505, AM464_20560, AUQ13_21565, BMA87_17500, BUE81_17200, BvCms2454_02009, BvCmsHHP001_00880, BvCmsKSNP120_02778, BvCmsKSP076_04015, BW690_14780, C5N07_14455, C9Z39_12310, CA593_25875, CI694_20445, CIG45_13010, D0X26_17735, D2185_16075, D3821_19610, D4638_22450, D4718_15390, D9D20_13050, D9D44_16075, D9G69_11750, D9J52_13020, DBQ99_18215, DJ503_07085, DL326_16140, DT034_15925, E2119_09030, E4K55_13820, E4K60_15665, E4K61_12850, EA213_10835, EAI52_07270, EC3234A_6c00760, EC3426_01483, ECTO6_03389, ED307_12710, EEP23_08605, EI021_13075, EI028_12695, EI041_12995, EIZ93_02940, EL75_3125, EL79_3219, EL80_3175, ELT20_10985, EPT01_08450, EXX71_13910, EYD11_16175, FV293_12780, GHR40_20735, GKF74_06475, GKF86_07920, GKF89_05980, GP689_15750, GQE34_06850, GQM17_21560, GRW42_10840, NCTC8500_03946, NCTC9045_04089, NCTC9062_04723, NCTC9969_03714, PGD_02673, RK56_025370, SAMEA3472047_02047, SAMEA3472080_00307, SAMEA3484427_03116, SAMEA3484429_03266, SAMEA3752559_01009, SAMEA3753300_04108, SK85_00657 Production host: ![]() ![]() References: UniProt: A0A037YBN4, UniProt: P23930*PLUS, apolipoprotein N-acyltransferase | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-LH9 / [( #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.85 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 0.1M MES pH 6.0, * %(v/v) MPD, 0.05-0.4 M sodium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.57 Å / Num. obs: 26629 / % possible obs: 99.34 % / Redundancy: 12.9 % / Biso Wilson estimate: 38.94 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.3→2.382 Å / Num. unique obs: 2578 / CC1/2: 0.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N6H Resolution: 2.3→46.57 Å / SU ML: 0.2367 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3107 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→46.57 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 |
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