+Open data
-Basic information
Entry | Database: PDB / ID: 6f56 | ||||||
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Title | Mutant of Human N-myristoyltransferase with bound myristoyl-CoA | ||||||
Components | Glycylpeptide N-tetradecanoyltransferase 1 | ||||||
Keywords | TRANSFERASE / N-Myristoyltransferase / mutant / parasite | ||||||
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: 1.9401987668 Å | ||||||
Authors | Brenk, R. / Kehrein, J. / Kersten, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Med.Chem. / Year: 2019 Title: How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study UsingN-Myristoyltransferases as a Model System. Authors: Kersten, C. / Fleischer, E. / Kehrein, J. / Borek, C. / Jaenicke, E. / Sotriffer, C. / Brenk, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f56.cif.gz | 347.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f56.ent.gz | 277.1 KB | Display | PDB format |
PDBx/mmJSON format | 6f56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/6f56 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/6f56 | HTTPS FTP |
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-Related structure data
Related structure data | 6eu5C 6ewfC 6fz2C 6fz3C 6fz5C 4c2yS 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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Unit cell |
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-Components
#1: Protein | Mass: 47596.762 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1, NMT / Production host: Escherichia coli (E. coli) References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase #2: Chemical | ChemComp-MYA / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-GOL / #5: 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: 2.28 Å3/Da / Density % sol: 45.99 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: PEG 4000 22 % Sodium citrate 0.1 M Glycerol 2.5 % |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 29, 2017 |
Radiation | Monochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→87.495 Å / Num. obs: 112254 / % possible obs: 92.8 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 26.7375608735 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.063 / Rrim(I) all: 0.119 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.94→1.974 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4257 / CC1/2: 0.801 / Rpim(I) all: 0.541 / Rrim(I) all: 1.003 / % possible all: 72.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4C2Y Resolution: 1.9401987668→87.495 Å / SU ML: 0.236556340204 / Cross valid method: FREE R-VALUE / σ(F): 1.34087675499 / Phase error: 28.716419119
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.4604115534 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9401987668→87.495 Å
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Refine LS restraints |
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LS refinement shell |
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