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Yorodumi- PDB-8fi4: Crystal Structure of Glycylpeptide N-tetradecanoyltransferase (N-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fi4 | |||||||||
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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 1) | |||||||||
Components | Glycylpeptide N-tetradecanoyltransferase | |||||||||
Keywords | TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | |||||||||
Function / homology | TETRADECANOYL-COA / : Function and homology information | |||||||||
Biological species | Leishmania major strain Friedlin (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Crystal Structure of Glycylpeptide N-tetradecanoyltransferase (N-myristoyl transferase) (NMT) from Leishmania major Friedlin bound to tetradecanoyl-CoA (Orthorhombic P Form 1) Authors: Lovell, S. / Battaile, K.P. / Staker, B.L. / Liu, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fi4.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fi4.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 8fi4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/8fi4 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/8fi4 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) Leishmania major strain Friedlin (eukaryote) Gene: LMJFC_320006100 / Plasmid: LemaA.18219.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8J9XEH4 |
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#2: Chemical | ChemComp-MYA / |
#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: 1.99 Å3/Da / Density % sol: 38.26 % |
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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_02, Cryo: 20% PEG 200. MYA ligand was acquired from the expression host and ...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_02, Cryo: 20% PEG 200. 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: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å |
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→46.39 Å / Num. obs: 36370 / % possible obs: 98.4 % / Redundancy: 10.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.039 / Rrim(I) all: 0.128 / Χ2: 0.95 / Net I/σ(I): 12.2 / Num. measured all: 387821 |
Reflection shell | Resolution: 1.8→1.84 Å / % possible obs: 97.2 % / Redundancy: 11.5 % / Rmerge(I) obs: 1.388 / Num. measured all: 23955 / Num. unique obs: 2090 / CC1/2: 0.803 / Rpim(I) all: 0.423 / Rrim(I) all: 1.452 / Χ2: 0.87 / Net I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.39 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.65 / Stereochemistry target values: ML
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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→46.39 Å
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Refine LS restraints |
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LS refinement shell |
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