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Yorodumi- PDB-8q24: HsNMT1 in complex with both MyrCoA and (DAB)SFSKPR inhibitor peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q24 | |||||||||||||||
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Title | HsNMT1 in complex with both MyrCoA and (DAB)SFSKPR inhibitor 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 / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / Late Phase of HIV Life Cycle / 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 / 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: 1.9 Å | |||||||||||||||
Authors | Dian, C. / Giglione, C. / Meinnel, T. | |||||||||||||||
Funding support | France, 4items
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Citation | Journal: to be published Title: HsNMT1 in complex with both MyrCoA and Dab-SFSKPR inhibitor peptide Authors: Dian, C. / Giglione, C. / Meinnel, T. / Riviere, F. / Dutheil, F.R. / Monassa, P. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q24.cif.gz | 231.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q24.ent.gz | 148.9 KB | Display | PDB format |
PDBx/mmJSON format | 8q24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q24_validation.pdf.gz | 929.1 KB | Display | wwPDB validaton report |
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Full document | 8q24_full_validation.pdf.gz | 939.9 KB | Display | |
Data in XML | 8q24_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 8q24_validation.cif.gz | 51.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/8q24 ftp://data.pdbj.org/pub/pdb/validation_reports/q2/8q24 | HTTPS FTP |
-Related structure data
Related structure data | 5o9tS S: Starting model for refinement |
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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 ABEC
#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): ROSETTA2 PLYSS References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase #2: Protein/peptide | Mass: 822.952 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 4 types, 496 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: 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: 2.11 Å3/Da / Density % sol: 41.64 % |
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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, 0.1 M MgCL2, 0.1 M 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: 0.97563 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 15, 2020 / Details: KB mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97563 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.75 Å / Num. obs: 124527 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 1 / Rpim(I) all: 0.023 / Rsym value: 0.057 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4176 / CC1/2: 0.973 / Rpim(I) all: 0.233 / Rsym value: 0.584 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5O9T Resolution: 1.9→48.75 Å / SU ML: 0.1939 / Cross valid method: FREE R-VALUE / σ(F): 0.46 / Phase error: 23.5369 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: 38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→48.75 Å
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Refine LS restraints |
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LS refinement shell |
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