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Yorodumi- PDB-3jtk: Crystal Structure of human type-I N-myristoyltransferase with bou... -
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-Basic information
Entry | Database: PDB / ID: 3jtk | ||||||
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Title | Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and inhibitor DDD90055 | ||||||
Components | Glycylpeptide N-tetradecanoyltransferase 1 | ||||||
Keywords | TRANSFERASE / N-myristoyltransferase / NMT1 / Acyltransferase / Phosphoprotein / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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 / 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: 1.61 Å | ||||||
Authors | Qiu, W. / Hutchinson, A. / Wernimont, A. / Lin, Y.-H. / Kania, A. / Ravichandran, M. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Arrowsmith, C.H. ...Qiu, W. / Hutchinson, A. / Wernimont, A. / Lin, Y.-H. / Kania, A. / Ravichandran, M. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Wyatt, P.G. / Ferguson, M.A.J. / Frearson, J.A. / Brand, S.Y. / Robinson, D.A. / Bochkarev, A. / Hui, R. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and inhibitor DDD90055 Authors: Qiu, W. / Hutchinson, A. / Wernimont, A. / Lin, Y.-H. / Kania, A. / Ravichandran, M. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A. ...Authors: Qiu, W. / Hutchinson, A. / Wernimont, A. / Lin, Y.-H. / Kania, A. / Ravichandran, M. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Wyatt, P.G. / Ferguson, M.A.J. / Frearson, J.A. / Brand, S.Y. / Robinson, D.A. / Bochkarev, A. / Hui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jtk.cif.gz | 193.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jtk.ent.gz | 149.8 KB | Display | PDB format |
PDBx/mmJSON format | 3jtk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/3jtk ftp://data.pdbj.org/pub/pdb/validation_reports/jt/3jtk | HTTPS FTP |
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-Related structure data
Related structure data | 3iu1S S: Starting model for refinement |
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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
#1: Protein | Mass: 44541.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NMT, NMT1 / Production host: Escherichia coli (E. coli) References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase #2: Chemical | #3: Chemical | ChemComp-X55 / ( | #4: 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: 2.3 Å3/Da / Density % sol: 46.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: 19% PEG3350, 0.2M di-ammonium hydrogen citrate, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→40 Å / Num. all: 108441 / Num. obs: 106602 / % possible obs: 98.3 % / Redundancy: 6.54 % / Rmerge(I) obs: 0.067 / Rsym value: 0.038 / Net I/σ(I): 16.68 |
Reflection shell | Resolution: 1.61→1.71 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.4437 / Mean I/σ(I) obs: 2.52 / Num. unique all: 18516 / Rsym value: 0.481 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3IU1 Resolution: 1.61→19.76 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.926 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.913 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→19.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.647 Å / Total num. of bins used: 20
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