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Yorodumi- PDB-5o9v: HsNMT1 in complex with CoA and Myristoylated-GGCFSKPK octapeptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o9v | |||||||||
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Title | HsNMT1 in complex with CoA and Myristoylated-GGCFSKPK octapeptide | |||||||||
Components |
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Keywords | TRANSFERASE / GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 1 N-MYRISTOYLTRANSFERASE 1 / N-MYRISTOYLTRANSFERASE TYPE1 / NMT1 / NMT / ACYLTRANSFERASE / MYR-PEPTIDE / COA / MYR-COA / MYRISTOYL / GNAT | |||||||||
Function / homology | Function and homology information myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / 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 / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / 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 / Oxidoreductases / oxidoreductase activity, acting on NAD(P)H / execution phase of apoptosis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 2 iron, 2 sulfur cluster binding / Inactivation, recovery and regulation of the phototransduction cascade / flavin adenine dinucleotide binding / in utero embryonic development / mitochondrial inner membrane / endoplasmic reticulum / mitochondrion / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å | |||||||||
Authors | Dian, C. / Meinnel, T. / Giglione, C. | |||||||||
Funding support | France, 2items
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Citation | Journal: Nat. Chem. Biol. / Year: 2018 Title: Structural and genomic decoding of human and plant myristoylomes reveals a definitive recognition pattern. Authors: Castrec, B. / Dian, C. / Ciccone, S. / Ebert, C.L. / Bienvenut, W.V. / Le Caer, J.P. / Steyaert, J.M. / 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 | 5o9v.cif.gz | 192.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o9v.ent.gz | 149.9 KB | Display | PDB format |
PDBx/mmJSON format | 5o9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/5o9v ftp://data.pdbj.org/pub/pdb/validation_reports/o9/5o9v | HTTPS FTP |
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-Related structure data
Related structure data | 5o9sC 5o9tC 5o9uC 4c2zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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 ABCD
#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 derivative / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2(DE3) pLysS References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase #2: Protein/peptide | Mass: 824.988 Da / Num. of mol.: 2 / Fragment: UNP residues 2-9 / Source method: obtained synthetically Details: Synthetic octapeptide GGCFSKPK modified by NMT1 to (MYR)GGCFSKPK. Source: (synth.) Homo sapiens (human) / References: UniProt: Q96NN9, Oxidoreductases |
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-Non-polymers , 5 types, 505 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.16 Å3/Da / Density % sol: 43.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 22% PEG8000, 0.1M sodium citrate pH5.6, 0.1 M magnesium chloride, 0.1M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryo Oxford |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.96112 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 4, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96112 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.69 Å / Num. obs: 42368 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 26.79 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.027 / Rsym value: 0.082 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 5.6 / Num. unique obs: 4029 / CC1/2: 0.93 / Rpim(I) all: 0.136 / Rsym value: 0.378 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4C2Z Resolution: 2.201→48.689 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.201→48.689 Å
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Refine LS restraints |
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LS refinement shell |
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