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- PDB-4ucm: CRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT... -

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Basic information

Entry
Database: PDB / ID: 4ucm
TitleCRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT) WITH BOUND MYRISTOYL-COA AND A FRAGMENT
ComponentsGLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
KeywordsTRANSFERASE / NMT / MYRISTOYLTRANSFERASE / ACYLTRANSFERASE / DRUG DISCOVERY / FRAGMENT
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane / metal ion binding / 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 / Chem-X6W / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsRobinson, D.A. / Wyatt, P.G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Identification and Structure Solution of Fragment Hits Against Kinetoplastid N-Myristoyltransferase
Authors: Robinson, D.A. / Wyatt, P.G.
History
DepositionDec 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Apr 22, 2020Group: Database references / Other / Category: pdbx_database_status / pdbx_related_exp_data_set / Item: _pdbx_database_status.status_code_sf
Revision 1.3Dec 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)51,6923
Polymers50,5131
Non-polymers1,1792
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.126, 91.207, 53.651
Angle α, β, γ (deg.)90.00, 112.67, 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: RESIDUES 5-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / 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-X6W / methyl-3-methyl-5-phenyl-2H-pyrazol-4-methyl amine


Mass: 201.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.29 Å3/Da / Density % sol: 0.46 % / Description: NONE
Crystal growpH: 5.5 / Details: 25.9%PEG1500,0.2M NACL, 0.1M NACACODYLATE, PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97887
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 2.32→44 Å / Num. obs: 17931 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 24
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 10 / % possible all: 87.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H5Z

3h5z


Resolution: 2.32→49.51 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.893 / SU B: 16.809 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.575 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26743 898 5 %RANDOM
Rwork0.21143 ---
obs0.21427 16896 95.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.021 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å2-0.41 Å2
2---0.58 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.32→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 78 102 3533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223534
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.9794812
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6365410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31623.743171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09615564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1231522
X-RAY DIFFRACTIONr_chiral_restr0.070.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212733
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_it0.391.52069
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74123364
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.97931465
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5754.51448
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 70 -
Rwork0.24 1278 -
obs--98.39 %
Refinement TLS params.Method: refined / Origin x: 18.724 Å / Origin y: 0.646 Å / Origin z: 7.744 Å
111213212223313233
T0.0229 Å2-0.0176 Å20.0181 Å2-0.3387 Å20.011 Å2--0.1485 Å2
L0.7656 °2-0.0876 °20.0022 °2-0.8729 °20.196 °2--0.3505 °2
S0.001 Å °0.0967 Å °0.023 Å °0.1327 Å °-0.0045 Å °0.0091 Å °0.051 Å °-0.0059 Å °0.0035 Å °

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