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Open data
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Basic information
Entry | Database: PDB / ID: 4c2y | ||||||
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Title | Human N-myristoyltransferase (NMT1) with Myristoyl-CoA co-factor | ||||||
![]() | GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 1![]() | ||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thinon, E. / Serwa, R.A. / Brannigan, J.A. / Brassat, U. / Wright, M.H. / Heal, W.P. / Wilkinson, A.J. / Mann, D.J. / Tate, E.W. | ||||||
![]() | ![]() Title: Global Profiling of Co- and Post-Translationally N-Myristoylated Proteomes in Human Cells. Authors: Thinon, E. / Serwa, R.A. / Broncel, M. / Brannigan, J.A. / Brassat, U. / Wright, M.H. / Heal, W.P. / Wilkinson, A.J. / Mann, D.J. / Tate, E.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200.3 KB | Display | ![]() |
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PDB format | ![]() | 158.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4c2xC ![]() 4c2zC ![]() 3iu1S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 47605.688 Da / Num. of mol.: 2 / Fragment: RESIDUES 109-496 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P30419, ![]() |
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-Non-polymers , 5 types, 815 molecules ![](data/chem/img/MYA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/GOL.gif)
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#2: Chemical | #3: Chemical | #4: Chemical | ![]() #5: Chemical | ChemComp-GOL / ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % / Description: NONE |
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Crystal grow![]() | pH: 4.5 Details: 22.5% PEG 4000, 5 MM NICL2, 100 MM NA CITRATE PH 4.5, 2.5% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.64→72 Å / Num. obs: 98990 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.64→1.67 Å / Redundancy: 6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.4 / % possible all: 85 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3IU1 Resolution: 1.64→89.24 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.139 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.957 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→89.24 Å
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Refine LS restraints |
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