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Yorodumi- PDB-7owo: HsNMT1 in complex with both MyrCoA and N-acetylated KSFSKPR peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 7owo | ||||||||||||
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Title | HsNMT1 in complex with both MyrCoA and N-acetylated KSFSKPR peptide | ||||||||||||
Components |
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Keywords | TRANSFERASE / E-MYRISTOYLATION / NMT / MYRISTOYLTRANSFERASE TYPE1 / ACYLTRANSFERASE / GNAT / GCN5-RELATED N-ACETYLTRANSFERASES | ||||||||||||
Function / homology | Function and homology information myristoyltransferase activity / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / Late Phase of HIV Life Cycle / cellular ketone metabolic process / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane ...myristoyltransferase activity / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / Late Phase of HIV Life Cycle / cellular ketone metabolic process / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Inactivation, recovery and regulation of the phototransduction cascade / in utero embryonic development / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||||||||
Authors | Dian, C. / Giglione, C. / Meinnel, T. | ||||||||||||
Funding support | France, 3items
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Citation | Journal: J.Mol.Biol. / Year: 2022 Title: Structural and Large-scale Analysis Unveil the Intertwined Paths Promoting NMT-catalyzed Lysine and Glycine Myristoylation. Authors: Riviere, F. / Dian, C. / Dutheil, R.F. / Monassa, P. / Giglione, C. / Meinnel, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7owo.cif.gz | 241.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7owo.ent.gz | 154.4 KB | Display | PDB format |
PDBx/mmJSON format | 7owo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/7owo ftp://data.pdbj.org/pub/pdb/validation_reports/ow/7owo | HTTPS FTP |
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-Related structure data
Related structure data | 7owmC 7ownC 7owpC 7owqC 7owrC 7owuC 5o9tS S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABDF
#1: Protein | Mass: 46465.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1, NMT / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): ROSETTA2 PLYSS References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase #2: Protein/peptide | Mass: 878.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 5 types, 682 molecules
#3: Chemical | #4: Chemical | ChemComp-COA / | #5: Chemical | #6: Chemical | ChemComp-MYR / | #7: 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: 2.15 Å3/Da / Density % sol: 42.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 23% PEG 6K, 100mM NaCitrate 5.6, 100mM MgCl2, 100mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97856 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 4, 2020 / Details: K/B Mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.72 Å / Num. obs: 79532 / % possible obs: 97.19 % / Redundancy: 13.2 % / Biso Wilson estimate: 18.17 Å2 / CC1/2: 0.9985 / Rpim(I) all: 0.031 / Rsym value: 0.11 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.7→1.75 Å / Redundancy: 12.31 % / Mean I/σ(I) obs: 1.872 / Num. unique obs: 3977 / CC1/2: 0.7665 / Rpim(I) all: 0.409 / Rsym value: 1.401 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5O9T Resolution: 1.7→48.72 Å / SU ML: 0.1802 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.054 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: 26.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→48.72 Å
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Refine LS restraints |
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LS refinement shell |
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