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- PDB-8fi6: Crystal Structure of Glycylpeptide N-tetradecanoyltransferase (N-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fi6 | |||||||||
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Title | Crystal Structure of Glycylpeptide N-tetradecanoyltransferase (N-myristoyl transferase) (NMT) from Leishmania major Friedlin bound to tetradecanoyl-CoA (Orthorhombic P Form 3) | |||||||||
![]() | Glycylpeptide N-tetradecanoyltransferase | |||||||||
![]() | TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | |||||||||
Function / homology | TETRADECANOYL-COA / : ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Glycylpeptide N-tetradecanoyltransferase (N-myristoyl transferase) (NMT) from Leishmania major Friedlin bound to tetradecanoyl-CoA (Orthorhombic P Form 3) Authors: Lovell, S. / Battaile, K.P. / Staker, B.L. / Liu, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.5 KB | Display | ![]() |
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PDB format | ![]() | 77.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 636.5 KB | Display | ![]() |
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Full document | ![]() | 636.7 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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: 49174.914 Da / Num. of mol.: 1 / Mutation: K148R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: LMJFC_320006100 / Plasmid: LemaA.18219.a.B2 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-MYA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1 M Bicine, 20% PEG 6000, LemaA.18219.a.B2.PS38707 at 11.17 mg/mL. Tray: Tray 383B3/1 mM Perez-1, Puck: HR00406_03, Cryo: 20% MPD. MYA ligand was acquired from the expression host and not ...Details: 0.1 M Bicine, 20% PEG 6000, LemaA.18219.a.B2.PS38707 at 11.17 mg/mL. Tray: Tray 383B3/1 mM Perez-1, Puck: HR00406_03, Cryo: 20% MPD. MYA ligand was acquired from the expression host and not added prior to crystallization. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 10, 2022 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.78 Å / Num. obs: 43124 / % possible obs: 99.7 % / Redundancy: 9.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.028 / Rrim(I) all: 0.085 / Χ2: 1.01 / Net I/σ(I): 14.9 / Num. measured all: 393008 |
Reflection shell | Resolution: 1.8→1.84 Å / % possible obs: 99.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 1.323 / Num. measured all: 24005 / Num. unique obs: 2515 / CC1/2: 0.65 / Rpim(I) all: 0.447 / Rrim(I) all: 1.399 / Χ2: 0.98 / Net I/σ(I) obs: 1.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→47.22 Å
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Refine LS restraints |
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LS refinement shell |
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