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- PDB-5npq: Human N-myristoyltransferase 1 (MNT1) with Myristoyl-CoA analogue... -

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Basic information

Entry
Database: PDB / ID: 5npq
TitleHuman N-myristoyltransferase 1 (MNT1) with Myristoyl-CoA analogue X10 bound
ComponentsGlycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE / N-myristoylation / Myristol-CoA analogue / UV active / chemical probe
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 / ketone metabolic process / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity ...myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / Late Phase of HIV Life Cycle / ketone metabolic process / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane / eNOS activation / 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
Chem-94Q / Glycylpeptide N-tetradecanoyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.372 Å
AuthorsShen, M. / Perez-Dorado, I. / Fedoryshchak, R. / Tate, E.W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
MMV United Kingdom
Lee family scholarship United Kingdom
CitationJournal: To be published
Title: Human N-myristoyltransferase 1 (MNT1) with Myristoyl-CoA analogue X10 bound.
Authors: Shen, M. / Perez-Dorado, I. / Fedoryshchak, R. / Tate, E.W.
History
DepositionApr 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 1
B: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,32310
Polymers90,9072
Non-polymers2,4178
Water2,324129
1
A: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6625
Polymers45,4531
Non-polymers1,2084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6625
Polymers45,4531
Non-polymers1,2084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.972, 177.454, 58.244
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 115:132 or (resid 133 and (name...
21(chain B and (resseq 115:169 or resseq 171:181 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGVALVAL(chain A and (resseq 115:132 or (resid 133 and (name...AA115 - 13210 - 27
12ASNASNASNASN(chain A and (resseq 115:132 or (resid 133 and (name...AA13328
13ARGARGGLNGLN(chain A and (resseq 115:132 or (resid 133 and (name...AA115 - 49610 - 391
14ARGARGGLNGLN(chain A and (resseq 115:132 or (resid 133 and (name...AA115 - 49610 - 391
15ARGARGGLNGLN(chain A and (resseq 115:132 or (resid 133 and (name...AA115 - 49610 - 391
16ARGARGGLNGLN(chain A and (resseq 115:132 or (resid 133 and (name...AA115 - 49610 - 391
21ARGARGLEULEU(chain B and (resseq 115:169 or resseq 171:181 or (resid...BB115 - 16910 - 64
22GLUGLUVALVAL(chain B and (resseq 115:169 or resseq 171:181 or (resid...BB171 - 18166 - 76
23ARGARGARGARG(chain B and (resseq 115:169 or resseq 171:181 or (resid...BB18984
24ARGARGGLNGLN(chain B and (resseq 115:169 or resseq 171:181 or (resid...BB115 - 49610 - 391
25ARGARGGLNGLN(chain B and (resseq 115:169 or resseq 171:181 or (resid...BB115 - 49610 - 391
26ARGARGGLNGLN(chain B and (resseq 115:169 or resseq 171:181 or (resid...BB115 - 49610 - 391
27ARGARGGLNGLN(chain B and (resseq 115:169 or resseq 171:181 or (resid...BB115 - 49610 - 391

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Components

#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: 45453.348 Da / Num. of mol.: 2 / Fragment: human N-myristoyltransferase
Mutation: This protein was produced with an N-terminal His-Tag followed by a 3C protease site. The His-tag was cleaved with 3C protease for crystallization leaving 3 residues that are followed by 109- ...Mutation: This protein was produced with an N-terminal His-Tag followed by a 3C protease site. The His-tag was cleaved with 3C protease for crystallization leaving 3 residues that are followed by 109-496 amino acids of the NMT1
Source method: isolated from a genetically manipulated source
Details: This protein was produced with an N-terminal His-Tag followed by a 3C protease site. The His-tag was cleaved with 3C protease for crystallization leaving 3 residues that are followed by 109- ...Details: This protein was produced with an N-terminal His-Tag followed by a 3C protease site. The His-tag was cleaved with 3C protease for crystallization leaving 3 residues that are followed by 109-496 amino acids of the NMT1. The 3 residues preceding the NMT1 were not modeled as they were flexible and not observed in the electron density map. Residues 109-114, 182-188, 308-319 and 407-414 of the NMT1 chain A and residues 109-114 and 312-318 of the NMT1 chain B were not modeled because they were disordered and cannot be seen in the electron density map.
Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1, NMT / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRareS
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Fragment: X10-CoA
Mutation: X10-CoA is an analogue of Myristoyl-CoA with a diazirine on the 10th carbon of the fatty acid chain and an alkyne at the end
Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-94Q / ~{S}-[2-[3-[[(2~{S})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 9-(3-but-3-ynyl-1,2-diazirin-3-yl)nonanethioate / Myristoyl-CoA analogue X10


Mass: 999.856 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H56N9O17P3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M NaCit pH 4.5, 5mM NiCl2, 2.5% glycerol and PEG 4K 18% Protein concentration: 7.05 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.372→177.454 Å / Num. obs: 34474 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 32.66 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.076 / Net I/σ(I): 9.3
Reflection shellResolution: 2.372→2.413 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1709 / CC1/2: 0.661 / Rpim(I) all: 0.353 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Coot0.8.6model building
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
PHASER2.7.17phasing
XDSNovember 1, 2016data reduction
Aimless0.5.29data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4C2Y

4c2y


Resolution: 2.372→88.727 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.23
Details: The 3 residues preceding the NMT1 are left from the His-Tag cleavage and were not modeled as they were flexible and not observed in the electron density map. Residues 109-114, 182-188, 308- ...Details: The 3 residues preceding the NMT1 are left from the His-Tag cleavage and were not modeled as they were flexible and not observed in the electron density map. Residues 109-114, 182-188, 308-319 and 407-414 of the NMT1 chain A, and residues 109-114 and 312-318 of the NMT1 chain B were not modeled because they were disordered and cannot be seen in the electron density map
RfactorNum. reflection% reflection
Rfree0.2606 1735 5.04 %
Rwork0.1991 --
obs0.2022 34414 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.08 Å2 / Biso mean: 34.6127 Å2 / Biso min: 14.18 Å2
Refinement stepCycle: final / Resolution: 2.372→88.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5889 0 156 129 6174
Biso mean--34.03 30.01 -
Num. residues----730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086212
X-RAY DIFFRACTIONf_angle_d1.0398461
X-RAY DIFFRACTIONf_chiral_restr0.06921
X-RAY DIFFRACTIONf_plane_restr0.0071057
X-RAY DIFFRACTIONf_dihedral_angle_d14.8713647
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3309X-RAY DIFFRACTION6.228TORSIONAL
12B3309X-RAY DIFFRACTION6.228TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3723-2.44210.37951360.304826792815
2.4421-2.52090.34841370.272726822819
2.5209-2.6110.3251250.256726912816
2.611-2.71560.34071330.247226862819
2.7156-2.83920.27941460.227226952841
2.8392-2.98890.26271460.217627042850
2.9889-3.17610.26421640.196226712835
3.1761-3.42140.2461630.182827042867
3.4214-3.76570.25921220.175727252847
3.7657-4.31060.22861570.158727382895
4.3106-5.43080.2071510.159527842935
5.4308-88.78910.25731550.206429203075

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