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- PDB-6f56: Mutant of Human N-myristoyltransferase with bound myristoyl-CoA -

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Basic information

Entry
Database: PDB / ID: 6f56
TitleMutant of Human N-myristoyltransferase with bound myristoyl-CoA
ComponentsGlycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE / N-Myristoyltransferase / mutant / parasite
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 / cytoplasm / cytosol
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9401987668 Å
AuthorsBrenk, R. / Kehrein, J. / Kersten, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: J.Med.Chem. / Year: 2019
Title: How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study UsingN-Myristoyltransferases as a Model System.
Authors: Kersten, C. / Fleischer, E. / Kehrein, J. / Borek, C. / Jaenicke, E. / Sotriffer, C. / Brenk, R.
History
DepositionNov 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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

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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: Glycylpeptide N-tetradecanoyltransferase 1
D: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,22521
Polymers190,3874
Non-polymers4,83817
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13400 Å2
ΔGint-114 kcal/mol
Surface area65210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.190, 159.130, 174.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 47596.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1, NMT / Production host: Escherichia coli (E. coli)
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Chemical
ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: PEG 4000 22 % Sodium citrate 0.1 M Glycerol 2.5 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 29, 2017
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.94→87.495 Å / Num. obs: 112254 / % possible obs: 92.8 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 26.7375608735 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.063 / Rrim(I) all: 0.119 / Net I/σ(I): 11.3
Reflection shellResolution: 1.94→1.974 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4257 / CC1/2: 0.801 / Rpim(I) all: 0.541 / Rrim(I) all: 1.003 / % possible all: 72.2

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Processing

Software
NameVersionClassification
autoPROC1.1.7data collection
PHASER2.8.0phasing
Coot0.8.2model building
PHENIX1.12_2829refinement
XDSBUILT=20170615data reduction
XSCALEBUILT=20170615data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C2Y

4c2y


Resolution: 1.9401987668→87.495 Å / SU ML: 0.236556340204 / Cross valid method: FREE R-VALUE / σ(F): 1.34087675499 / Phase error: 28.716419119
RfactorNum. reflection% reflection
Rfree0.239438285168 5517 4.92000642089 %
Rwork0.199550279057 --
obs0.201532698232 112134 92.6650690026 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.4604115534 Å2
Refinement stepCycle: LAST / Resolution: 1.9401987668→87.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12532 0 310 464 13306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032342561794313264
X-RAY DIFFRACTIONf_angle_d0.69058742812118033
X-RAY DIFFRACTIONf_chiral_restr0.04752504522961949
X-RAY DIFFRACTIONf_plane_restr0.004171012094662259
X-RAY DIFFRACTIONf_dihedral_angle_d17.65665516064978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9402-1.96220.3575177888821000.3473761957192182X-RAY DIFFRACTION57.6845298281
1.9622-1.98530.3483771824751820.2814707158193782X-RAY DIFFRACTION99.7483643684
1.9853-2.00950.3330806763792030.274912009933800X-RAY DIFFRACTION99.875249501
2.0095-2.0350.3160371029991880.2601421624093758X-RAY DIFFRACTION99.7976732423
2.035-2.06180.3208043470381380.2698394507952542X-RAY DIFFRACTION93.7062937063
2.0618-2.090.370570335025260.343839780733507X-RAY DIFFRACTION72.1244925575
2.09-2.11990.3064337673281890.2358882935333766X-RAY DIFFRACTION99.6723790323
2.1199-2.15150.3087752764412100.2341685119893794X-RAY DIFFRACTION99.8503740648
2.1515-2.18510.3143681448851850.2309445718173764X-RAY DIFFRACTION99.8482932996
2.1851-2.2210.2964119101761980.2220363258413812X-RAY DIFFRACTION99.9252429604
2.221-2.25930.293028359767930.2522567777781703X-RAY DIFFRACTION44.7099825741
2.2593-2.30040.2887036733532020.2197510505423767X-RAY DIFFRACTION99.7988433493
2.3004-2.34460.271612128571810.2170843889613839X-RAY DIFFRACTION99.8757763975
2.3446-2.39250.2736328945262010.2154599620043767X-RAY DIFFRACTION99.7987927565
2.3925-2.44450.258561584011850.2105406680783832X-RAY DIFFRACTION99.9005222581
2.4445-2.50140.2551370259362100.2090856523193783X-RAY DIFFRACTION99.8749374687
2.5014-2.56390.2663601324882230.2206237614473796X-RAY DIFFRACTION99.751799454
2.5639-2.63320.2782091680452110.2226895766793818X-RAY DIFFRACTION99.9255952381
2.6332-2.71070.2814134885331780.2158532032953792X-RAY DIFFRACTION99.8993457474
2.7107-2.79820.2587923503831970.2137238647463862X-RAY DIFFRACTION99.9261447563
2.7982-2.89820.3125545526811940.2101312959033835X-RAY DIFFRACTION99.9751861042
2.8982-3.01430.2513008006941960.2023904228883836X-RAY DIFFRACTION99.8761456527
3.0143-3.15150.2447051348521970.2093429422583823X-RAY DIFFRACTION99.9005964215
3.1515-3.31760.2383893948982020.1961056574833872X-RAY DIFFRACTION99.8040176384
3.3176-3.52550.2193023165591940.1887793949043865X-RAY DIFFRACTION99.8769685039
3.5255-3.79770.2446174731511910.1799814406523861X-RAY DIFFRACTION100
3.7977-4.17990.1685952910371940.1605732417923930X-RAY DIFFRACTION100
4.1799-4.78470.1557127083962310.1441515838743869X-RAY DIFFRACTION99.6839290056
4.7847-6.0280.1891627839032120.1735249790493928X-RAY DIFFRACTION99.5192307692
6.028-87.58410.242446956312060.206600360054132X-RAY DIFFRACTION99.2677345538

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