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- PDB-4c2x: Human N-myristoyltransferase isoform 2 (NMT2) -

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Basic information

Entry
Database: PDB / ID: 4c2x
TitleHuman N-myristoyltransferase isoform 2 (NMT2)
ComponentsGLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 2
KeywordsTRANSFERASE / MYRISTOYLATION
Function / homology
Function and homology information


intracellular transport of virus / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / regulation of opsin-mediated signaling pathway / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / host cell / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Membrane binding and targetting of GAG proteins / Inactivation, recovery and regulation of the phototransduction cascade ...intracellular transport of virus / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / regulation of opsin-mediated signaling pathway / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / host cell / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Membrane binding and targetting of GAG proteins / Inactivation, recovery and regulation of the phototransduction cascade / Golgi apparatus / 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
2-oxopentadecyl-CoA / Glycylpeptide N-tetradecanoyltransferase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsThinon, E. / Serwa, R.A. / Brannigan, J.A. / Brassat, U. / Wright, M.H. / Heal, W.P. / Wilkinson, A.J. / Mann, D.J. / Tate, E.W.
CitationJournal: Nat.Commun. / Year: 2014
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
DepositionAug 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6073
Polymers47,5911
Non-polymers1,0162
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.700, 72.320, 114.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 2 / / GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE / MYRISTOYL-COA\:PROTEIN N-MYRISTOYLTRANSFERASE 2 / NMT 2 ...GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE / MYRISTOYL-COA\:PROTEIN N-MYRISTOYLTRANSFERASE 2 / NMT 2 / PEPTIDE N-MYRISTOYLTRANSFERASE 2 / TYPE II N-MYRISTOYLTRANSFERASE


Mass: 47590.699 Da / Num. of mol.: 1 / Fragment: RESIDUES 112-498
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28 DERIVATIVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PRARES
References: UniProt: O60551, glycylpeptide N-tetradecanoyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NHW / 2-oxopentadecyl-CoA


Mass: 991.916 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H64N7O17P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsS-(2-OXO)PENTADECYLCOA (NHW): NON-HYDROLYSABLE MYRISTOYL-COA DERIVATIVE

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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: 2.26 Å3/Da / Density % sol: 45.5 % / Description: NONE
Crystal growpH: 5.5 / Details: 25% PEG 3350, 0.2M KCL, 100 MM NA CITRATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.33→57 Å / Num. obs: 18414 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.2
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0033refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IU1

3iu1


Resolution: 2.33→61.17 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 11.2 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R: 0.47 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28812 940 5.1 %RANDOM
Rwork0.21823 ---
obs0.22173 17427 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.429 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2---1.72 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.33→61.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 65 68 3315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193370
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.9814582
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9975395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99423.548155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.7915586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0781521
X-RAY DIFFRACTIONr_chiral_restr0.1120.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212527
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2485.4111559
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.2028.111949
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4525.4321811
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.326→2.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 57 -
Rwork0.326 1270 -
obs--99.7 %

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