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- PDB-1iyl: Crystal Structure of Candida albicans N-myristoyltransferase with... -

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Basic information

Entry
Database: PDB / ID: 1iyl
TitleCrystal Structure of Candida albicans N-myristoyltransferase with Non-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-R64 / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 1.3Oct 25, 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: Myristoyl-CoA:Protein N-Myristoyltransferase
B: Myristoyl-CoA:Protein N-Myristoyltransferase
C: Myristoyl-CoA:Protein N-Myristoyltransferase
D: Myristoyl-CoA:Protein N-Myristoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,9007
Polymers181,6864
Non-polymers1,2133
Water00
1
A: Myristoyl-CoA:Protein N-Myristoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8262
Polymers45,4221
Non-polymers4041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myristoyl-CoA:Protein N-Myristoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8262
Polymers45,4221
Non-polymers4041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Myristoyl-CoA:Protein N-Myristoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8262
Polymers45,4221
Non-polymers4041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Myristoyl-CoA:Protein N-Myristoyltransferase


Theoretical massNumber of molelcules
Total (without water)45,4221
Polymers45,4221
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Myristoyl-CoA:Protein N-Myristoyltransferase
B: Myristoyl-CoA:Protein N-Myristoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6524
Polymers90,8432
Non-polymers8092
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-23 kcal/mol
Surface area36080 Å2
MethodPISA, PQS
6
C: Myristoyl-CoA:Protein N-Myristoyltransferase
D: Myristoyl-CoA:Protein N-Myristoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2483
Polymers90,8432
Non-polymers4041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-21 kcal/mol
Surface area36410 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.277, 96.885, 269.277
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.: 4
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-R64 / (1-METHYL-1H-IMIDAZOL-2-YL)-(3-METHYL-4-{3-[(PYRIDIN-3-YLMETHYL)-AMINO]-PROPOXY}-BENZOFURAN-2-YL)-METHANONE


Mass: 404.462 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H24N4O3

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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: 3.35 Å3/Da / Density % sol: 63.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3350, lithium sulfate, 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
215-18 %(w/v)PEG33501reservoir
30.2 Mlithium sulfate1reservoir
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 28, 1998
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 40711 / Num. obs: 40711 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.4
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4020 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 50 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNX2002refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IYK

1iyk


Resolution: 3.2→40 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: B-GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.366 2050 5 %RANDOM
Rwork0.284 ---
all0.288 40638 --
obs0.288 40638 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.4476 Å2 / ksol: 0.232096 e/Å3
Displacement parametersBiso mean: 45.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12507 0 90 0 12597
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.422
X-RAY DIFFRACTIONc_scbond_it1.412
X-RAY DIFFRACTIONc_scangle_it2.232.5
LS refinement shellResolution: 3.2→3.31 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.418 201 5.1 %
Rwork0.327 3751 -
obs-3952 98.9 %
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shell
*PLUS
Highest resolution: 3.2 Å

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