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- PDB-7t0e: Cryptococcus neoformans protein farnesyltransferase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7t0e
TitleCryptococcus neoformans protein farnesyltransferase in complex with FPP and inhibitor 2b
Components
  • Protein farnesyltransferase subunit beta
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTransferase/Inhibitor / Inhibitor / Protein prenylyltransferase / Antifungal / TRANSFERASE / TRANSFERASE-Inhibitor complex
Function / homology
Function and homology information


prenylation / protein prenyltransferase activity / protein geranylgeranyltransferase type I / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / zinc ion binding
Similarity search - Function
Protein farnesyltransferase subunit beta / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid
Similarity search - Domain/homology
Chem-3FX / FARNESYL DIPHOSPHATE / Chem-XOA / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / Protein farnesyltransferase subunit beta
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii H99 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.223 Å
AuthorsWang, Y. / Shi, Y. / Beese, L.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5P01AI104533 United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structure-Guided Discovery of Potent Antifungals that Prevent Ras Signaling by Inhibiting Protein Farnesyltransferase.
Authors: Wang, Y. / Xu, F. / Nichols, C.B. / Shi, Y. / Hellinga, H.W. / Alspaugh, J.A. / Distefano, M.D. / Beese, L.S.
History
DepositionNov 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Protein farnesyltransferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,99666
Polymers97,7202
Non-polymers5,27664
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20610 Å2
ΔGint137 kcal/mol
Surface area29850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.830, 140.830, 130.069
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-586-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / variant


Mass: 40913.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii H99 (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_02229 / Production host: Escherichia coli (E. coli) / References: UniProt: J9VSJ6
#2: Protein Protein farnesyltransferase subunit beta / FTase-beta


Mass: 56806.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii H99 (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_05740 / Production host: Escherichia coli (E. coli) / References: UniProt: T2BPA1, protein farnesyltransferase

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Non-polymers , 6 types, 419 molecules

#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 58 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-3FX / (2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid


Mass: 237.316 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H19NO4S
#6: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#7: Chemical ChemComp-XOA / (5S)-4-({1-[(4-bromophenyl)methyl]-1H-imidazol-5-yl}methyl)-5-butyl-1-(3-chlorophenyl)piperazin-2-one


Mass: 515.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H28BrClN4O / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.3 Å3/Da / Density % sol: 62.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 100mM CAPSO pH9.5, 50-75mM Li2SO4, 200mM NaCl, 16%-21% PEG4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.223→37.41 Å / Num. obs: 64466 / % possible obs: 99.35 % / Redundancy: 6.1 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06256 / Rpim(I) all: 0.02756 / Rrim(I) all: 0.06853 / Net I/σ(I): 19.01
Reflection shellResolution: 2.223→2.302 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 2.74 / Num. unique obs: 6241 / CC1/2: 0.946 / CC star: 0.986 / Rpim(I) all: 0.334 / Rrim(I) all: 0.8378 / % possible all: 97.52

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SFX

3sfx


Resolution: 2.223→37.41 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 1997 3.11 %
Rwork0.1906 118271 -
obs0.1911 64317 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.75 Å2 / Biso mean: 54.2781 Å2 / Biso min: 31.04 Å2
Refinement stepCycle: final / Resolution: 2.223→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6369 0 334 355 7058
Biso mean--63.09 56.33 -
Num. residues----803
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.223-2.250.35551350.3207412694
2.25-2.280.2891200.3169444599
2.28-2.310.31571470.2969437299
2.31-2.340.30891440.29934367100
2.34-2.380.33391420.2701438599
2.38-2.420.25681200.26394410100
2.42-2.460.23831430.2522441399
2.46-2.50.28571420.2387435599
2.5-2.540.28291540.2374439499
2.54-2.590.23951360.2294402100
2.59-2.650.24421740.22444351100
2.65-2.70.25461230.22084448100
2.7-2.770.27331440.2162437299
2.77-2.840.25751250.21264386100
2.84-2.910.23441430.20574376100
2.91-30.24661490.20694412100
3-3.090.22251610.19944396100
3.1-3.210.21481270.2026427797
3.21-3.330.21991210.19394416100
3.33-3.490.18561660.1884414100
3.49-3.670.19281360.17884379100
3.67-3.90.19971500.16674435100
3.9-4.20.17811270.16154413100
4.2-4.620.18011550.15454377100
4.62-5.290.13751430.164420100
5.29-6.660.19341410.1851431698
6.66-37.410.15821240.1527441499

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