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- PDB-1iyk: Crystal structure of candida albicans N-myristoyltransferase with... -

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Basic information

Entry
Database: PDB / ID: 1iyk
TitleCrystal structure of candida albicans N-myristoyltransferase with myristoyl-COA and peptidic inhibitor
ComponentsMYRISTOYL-COA:PROTEIN N-MYRISTOYLTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane / cytosol
Similarity search - Function
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 / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase ...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 / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MIM / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsSogabe, S. / Fukami, T.A. / Morikami, K. / Shiratori, Y. / Aoki, Y. / D'Arcy, A. / Winkler, F.K. / Banner, D.W. / Ohtsuka, T.
CitationJournal: CHEM.BIOL. / Year: 2002
Title: Crystal Structures of Candida albicans N-Myristoyltransferase with Two Distinct Inhibitors
Authors: Sogabe, S. / Masubuchi, M. / Sakata, K. / Fukami, T.A. / Morikami, K. / Shiratori, Y. / Ebiike, H. / Kawasaki, K. / Aoki, Y. / Shimma, N. / D'Arcy, A. / Winkler, F.K. / Banner, D.W. / Ohtsuka, T.
History
DepositionAug 29, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 9, 2011Group: Advisory
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: MYRISTOYL-COA:PROTEIN N-MYRISTOYLTRANSFERASE
B: MYRISTOYL-COA:PROTEIN N-MYRISTOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9936
Polymers90,8432
Non-polymers3,1494
Water2,216123
1
A: MYRISTOYL-COA:PROTEIN N-MYRISTOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9963
Polymers45,4221
Non-polymers1,5752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MYRISTOYL-COA:PROTEIN N-MYRISTOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9963
Polymers45,4221
Non-polymers1,5752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10060 Å2
ΔGint-70 kcal/mol
Surface area35170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.696, 95.334, 176.549
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 MYRISTOYL-COA:PROTEIN N-MYRISTOYLTRANSFERASE / Glycylpeptide N-tetradecanoyltransferase


Mass: 45421.566 Da / Num. of mol.: 2 / Fragment: residues 60-451
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Plasmid: pkf19 / Production host: Escherichia coli (E. coli)
References: UniProt: P30418, 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-MIM / [CYCLOHEXYLETHYL]-[[[[4-[2-METHYL-1-IMIDAZOLYL-BUTYL]PHENYL]ACETYL]-SERYL]-LYSINYL]-AMINE


Mass: 596.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H52N6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3350, ammonium acetate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
160 mg/mlprotein1drop
210-12 %(w/v)PEG33501reservoir
30.2 Mammonium acetate1reservoir
450 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 2, 1996
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 41498 / Num. obs: 41498 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 23.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3159 / % possible all: 71.4
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 92.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNX2002refinement
RefinementMethod to determine structure: MIR / Resolution: 2.3→40 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2096 5.1 %RANDOM
Rwork0.192 ---
all0.206 41433 --
obs0.206 41433 92.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.6081 Å2 / ksol: 0.277519 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6420 0 212 123 6755
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.56
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 248 4.6 %
Rwork0.261 5087 -
obs--72.3 %
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Lowest resolution: 2.38 Å / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.244

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