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- PDB-3iu2: Crystal Structure of human type-I N-myristoyltransferase with bou... -

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Basic information

Entry
Database: PDB / ID: 3iu2
TitleCrystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and inhibitor DDD90096
ComponentsGlycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE / N-myristoyltransferase / NMT1 / Acyltransferas / 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 / ketone metabolic process / regulation of opsin-mediated signaling pathway / positive regulation of establishment of protein localization to mitochondrion / Activation, myristolyation of BID and translocation to mitochondria / 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 / positive regulation of establishment of protein localization to mitochondrion / 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
Chem-096 / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsQiu, 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)
CitationJournal: To be Published
Title: Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and inhibitor DDD90096
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
DepositionAug 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Other
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 1
B: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9246
Polymers89,0832
Non-polymers2,8414
Water12,520695
1
A: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9623
Polymers44,5411
Non-polymers1,4202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9623
Polymers44,5411
Non-polymers1,4202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.572, 77.739, 179.627
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


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 ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#3: Chemical ChemComp-096 / (2R)-2-{4-hydroxy-5-methoxy-2-[3-(4-methylpiperazin-1-yl)propyl]phenyl}-3-pyridin-3-yl-1,3-thiazolidin-4-one


Mass: 442.574 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H30N4O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→20 Å / Num. all: 86101 / Num. obs: 84453 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 6.59 % / Rmerge(I) obs: 0.06 / Rsym value: 0.035 / Net I/σ(I): 20.29
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 4.97 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 4.12 / Num. unique all: 11287 / Rsym value: 0.26 / % possible all: 88.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→19.6 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.674 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23488 4216 5 %RANDOM
Rwork0.20652 ---
obs0.20795 80093 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.614 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å20 Å2
2--0.69 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.73→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6235 0 188 695 7118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226684
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.999106
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4925776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59623.648307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49151124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4221540
X-RAY DIFFRACTIONr_chiral_restr0.0940.2983
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215064
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_it0.4741.53845
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89826286
X-RAY DIFFRACTIONr_scbond_it1.34432839
X-RAY DIFFRACTIONr_scangle_it2.224.52810
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.778 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 237 -
Rwork0.296 4508 -
obs--100 %

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