+Open data
-Basic information
Entry | Database: PDB / ID: 7own | ||||||||||||
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Title | HsNMT1 in complex with both MyrCoA and peptide AKSFSKPR | ||||||||||||
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: 2.1 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 | 7own.cif.gz | 230.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7own.ent.gz | 147.6 KB | Display | PDB format |
PDBx/mmJSON format | 7own.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/7own ftp://data.pdbj.org/pub/pdb/validation_reports/ow/7own | HTTPS FTP |
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-Related structure data
Related structure data | 7owmC 7owoC 7owpC 7owqC 7owrC 7owuC 6sk2S 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
#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: 923.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | 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: 2.21 Å3/Da / Density % sol: 44.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 22% PEG6K, 100mM Sodium Citrate pH 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: 0.98012 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 21, 2020 / Details: KB mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98012 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→48.77 Å / Num. obs: 55446 / % possible obs: 99.4 % / Redundancy: 14.9 % / Biso Wilson estimate: 26.31 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.046 / Rsym value: 0.168 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.01→2.06 Å / Redundancy: 13 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3702 / CC1/2: 0.792 / Rpim(I) all: 0.428 / Rsym value: 1.529 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SK2 Resolution: 2.1→48.77 Å / SU ML: 0.1994 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.6844 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: 32.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→48.77 Å
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Refine LS restraints |
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LS refinement shell |
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