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- PDB-2wuu: Structure of N-myristoyltransferase from L. donovani -

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Basic information

Entry
Database: PDB / ID: 2wuu
TitleStructure of N-myristoyltransferase from L. donovani
ComponentsN-MYRISTOYLTRANSFERASE
KeywordsTRANSFERASE / ACYLTRANSFERASE
Function / homology
Function and homology information


N-terminal protein myristoylation / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity
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 / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLEISHMANIA DONOVANI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsBrannigan, J.A. / Smith, B.A. / Yu, Z. / Hodgkinson, M.R. / Leatherbarrow, R.J. / Tate, E.W. / Brzozowski, A.M. / Smith, D.F. / Wilkinson, A.J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: N-Myristoyltransferase from Leishmania Donovani: Structural and Functional Characterisation of a Potential Drug Target for Visceral Leishmaniasis.
Authors: Brannigan, J.A. / Smith, B.A. / Yu, Z. / Brzozowski, A.M. / Hodgkinson, M.R. / Maroof, A. / Price, H.P. / Meier, F. / Leatherbarrow, R.J. / Tate, E.W. / Smith, D.F. / Wilkinson, A.J.
History
DepositionOct 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Refinement description / Version format compliance
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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-MYRISTOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6492
Polymers48,6571
Non-polymers9921
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.970, 90.131, 92.355
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 N-MYRISTOYLTRANSFERASE


Mass: 48657.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA DONOVANI (eukaryote) / Strain: LV9 / Variant: MHOM/ET/67/L28 / Plasmid: PET28-BASED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PRARES
References: UniProt: A4I7H1, UniProt: D0AB09*PLUS, glycylpeptide N-tetradecanoyltransferase
#2: Chemical ChemComp-NHW / 2-oxopentadecyl-CoA


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


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details(2-OXO)PENTADECYL-COA (NHW): NON-HYDROLYSABLE ANALOGUE OF MYRISTOYLCOA COFACTOR
Sequence detailsTHE SEQUENCE FOR THIS PROTEIN IS CURRENTLY DEPOSITED ONLY IN THE EMBL NUCLEOTIDE DATA BANK WITH ...THE SEQUENCE FOR THIS PROTEIN IS CURRENTLY DEPOSITED ONLY IN THE EMBL NUCLEOTIDE DATA BANK WITH ACCESSION FN555136 AND IS NOT CURRENTLY AVAILABLE FROM UNIPROT.

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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: 1.96 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growpH: 4
Details: 0.6 M LICL, 0.05 M NACITRATE PH 4.0, 20% (W/V) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.42→40 Å / Num. obs: 68150 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.8
Reflection shellResolution: 1.42→1.46 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / % possible all: 78.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NMT

1nmt


Resolution: 1.42→40 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.062 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. DISORDERED RESIDUES 1-10, 83-85, 334-339.SOME SIDECHAINS BUILT WITH ZERO OCCUPANCY
RfactorNum. reflection% reflectionSelection details
Rfree0.19055 3603 5 %RANDOM
Rwork0.1464 ---
obs0.14866 68150 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.371 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2---0.98 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.42→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3285 0 64 378 3727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223595
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0771.9724928
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1065451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10723.333165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91315587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1661523
X-RAY DIFFRACTIONr_chiral_restr0.1580.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212791
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_it2.4221.52121
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.45323477
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.85631474
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.5384.51433
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.61733595
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 225 -
Rwork0.27 3986 -
obs--78.78 %
Refinement TLS params.Method: refined / Origin x: -8.411 Å / Origin y: -23.9183 Å / Origin z: 18.212 Å
111213212223313233
T0.004 Å20.0019 Å20.0012 Å2-0.0244 Å20.0037 Å2--0.0041 Å2
L0.216 °20.1849 °20.0612 °2-0.7819 °20.0961 °2--0.1272 °2
S-0.0001 Å °0.0048 Å °0.0024 Å °-0.0465 Å °0.0094 Å °0.0044 Å °-0.0082 Å °0.0109 Å °-0.0093 Å °

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