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- PDB-5o9t: HsNMT1 in complex with CoA and acetylated-NCFSKPK peptide -

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Basic information

Entry
Database: PDB / ID: 5o9t
TitleHsNMT1 in complex with CoA and acetylated-NCFSKPK peptide
Components
  • 1IP-CYS-PHE-SER-LYS-PRO-ARG
  • Glycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE / 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 / 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
Aminopeptidase - #170 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase ...Aminopeptidase - #170 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsDian, C. / Meinnel, T. / Giglione, C.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR PalMyProt France
Fondation ARCSFI2011120111203841 France
CitationJournal: 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
DepositionJun 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase 1
B: Glycylpeptide N-tetradecanoyltransferase 1
C: 1IP-CYS-PHE-SER-LYS-PRO-ARG
D: 1IP-CYS-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,27612
Polymers94,8814
Non-polymers2,3958
Water6,630368
1
A: Glycylpeptide N-tetradecanoyltransferase 1
C: 1IP-CYS-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6386
Polymers47,4402
Non-polymers1,1984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-39 kcal/mol
Surface area16560 Å2
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase 1
D: 1IP-CYS-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6386
Polymers47,4402
Non-polymers1,1984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-40 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.221, 79.641, 178.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Glycylpeptide N-tetradecanoyltransferase 1 / / Myristoyl-CoA:protein N-myristoyltransferase 1 / Type I N-myristoyltransferase / Peptide N- ...Myristoyl-CoA:protein N-myristoyltransferase 1 / Type I N-myristoyltransferase / Peptide N-myristoyltransferase 1


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 1IP-CYS-PHE-SER-LYS-PRO-ARG


Mass: 975.018 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: N-acetylated peptide / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 376 molecules

#3: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 21% PEG 6000, 0.1M sodium citrate pH 5.6, 0.1M Magnesium chloride, 0.1M sodium chloride.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryo
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 1, 2016 / Details: Compound Refractive Lens
RadiationMonochromator: Diamond (C110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.15→48.8 Å / Num. obs: 46155 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.33 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.039 / Rsym value: 0.093 / Net I/σ(I): 14.7
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 4.6 / Num. unique obs: 4517 / CC1/2: 0.902 / Rpim(I) all: 0.19 / Rsym value: 0.433 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C2Z

4c2z


Resolution: 2.15→47.75 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 2288 4.96 %
Rwork0.1649 --
obs0.1674 46115 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6433 0 152 368 6953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086799
X-RAY DIFFRACTIONf_angle_d0.9479251
X-RAY DIFFRACTIONf_dihedral_angle_d15.4794148
X-RAY DIFFRACTIONf_chiral_restr0.0631011
X-RAY DIFFRACTIONf_plane_restr0.0061164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1501-2.19680.31611300.21862675X-RAY DIFFRACTION100
2.1968-2.24790.25641330.20092708X-RAY DIFFRACTION100
2.2479-2.30410.25761440.20082680X-RAY DIFFRACTION100
2.3041-2.36640.26921640.19092674X-RAY DIFFRACTION100
2.3664-2.43610.25091360.18552734X-RAY DIFFRACTION100
2.4361-2.51470.23331200.18072728X-RAY DIFFRACTION100
2.5147-2.60460.23321500.18162686X-RAY DIFFRACTION100
2.6046-2.70880.22581340.17692711X-RAY DIFFRACTION100
2.7088-2.83210.22181490.17682736X-RAY DIFFRACTION100
2.8321-2.98140.24051440.17582725X-RAY DIFFRACTION100
2.9814-3.16820.20291620.16632720X-RAY DIFFRACTION100
3.1682-3.41270.21161210.1592780X-RAY DIFFRACTION100
3.4127-3.7560.20631420.15042742X-RAY DIFFRACTION100
3.756-4.29920.18581420.13762782X-RAY DIFFRACTION100
4.2992-5.41540.1711530.13412808X-RAY DIFFRACTION100
5.4154-47.7620.21511640.17112938X-RAY DIFFRACTION99

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