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- PDB-3h5z: Crystal Structure of Leishmania major N-myristoyltransferase with... -

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Basic information

Entry
Database: PDB / ID: 3h5z
TitleCrystal Structure of Leishmania major N-myristoyltransferase with bound myristoyl-CoA
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / N-myristoyltransferase / NMT / Leishmania major / structural genomics / Structural Genomics Consortium / SGC / Acyltransferase
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / 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
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsQiu, W. / Hutchinson, A. / Lin, Y.-H. / Wernimont, A. / Mackenzie, F. / Ravichandran, M. / Cossar, D. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. ...Qiu, W. / Hutchinson, A. / Lin, Y.-H. / Wernimont, A. / Mackenzie, F. / Ravichandran, M. / Cossar, D. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Ferguson, M.A.J. / Fairlamb, A.H. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: Nature / Year: 2010
Title: N-myristoyltransferase inhibitors as new leads to treat sleeping sickness.
Authors: Frearson, J.A. / Brand, S. / McElroy, S.P. / Cleghorn, L.A. / Smid, O. / Stojanovski, L. / Price, H.P. / Guther, M.L. / Torrie, L.S. / Robinson, D.A. / Hallyburton, I. / Mpamhanga, C.P. / ...Authors: Frearson, J.A. / Brand, S. / McElroy, S.P. / Cleghorn, L.A. / Smid, O. / Stojanovski, L. / Price, H.P. / Guther, M.L. / Torrie, L.S. / Robinson, D.A. / Hallyburton, I. / Mpamhanga, C.P. / Brannigan, J.A. / Wilkinson, A.J. / Hodgkinson, M. / Hui, R. / Qiu, W. / Raimi, O.G. / van Aalten, D.M. / Brenk, R. / Gilbert, I.H. / Read, K.D. / Fairlamb, A.H. / Ferguson, M.A. / Smith, D.F. / Wyatt, P.G.
History
DepositionApr 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,55314
Polymers50,5131
Non-polymers1,04013
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.816, 91.549, 53.625
Angle α, β, γ (deg.)90.00, 111.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 50513.254 Da / Num. of mol.: 1 / Fragment: UNP residues 5-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LmjF32.0080 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4Q5S8, glycylpeptide N-tetradecanoyltransferase
#2: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 25.9% PEG1500, 0.2M NaCl, 0.1M NaCacodylate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.48→50 Å / Num. all: 69213 / Num. obs: 68305 / % possible obs: 98.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.6 Å2 / Rsym value: 0.103 / Net I/σ(I): 10.5
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1 / Num. unique all: 6433 / Rsym value: 0.777 / % possible all: 93.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2P6E

2p6e


Resolution: 1.49→39.92 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.613 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21958 3454 5.1 %RANDOM
Rwork0.1871 ---
obs0.1887 64818 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.389 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.02 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.49→39.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 78 365 3797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0223593
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.9724908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3615430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67823.714175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92615577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1251522
X-RAY DIFFRACTIONr_chiral_restr0.2470.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212792
X-RAY DIFFRACTIONr_mcbond_it1.461.52105
X-RAY DIFFRACTIONr_mcangle_it2.29423436
X-RAY DIFFRACTIONr_scbond_it3.29531488
X-RAY DIFFRACTIONr_scangle_it4.8484.51464
LS refinement shellResolution: 1.49→1.531 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 225 -
Rwork0.315 4157 -
obs--86.84 %

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