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- PDB-7t0b: Cryptococcus neoformans protein farnesyltransferase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7t0b
TitleCryptococcus neoformans protein farnesyltransferase in complex with FPP and inhibitor 2g
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 geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / 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 alpha-alpha toroid domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid
Similarity search - Domain/homology
Chem-3FX / FARNESYL DIPHOSPHATE / Chem-XO4 / 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: 2.026 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)103,91581
Polymers97,7202
Non-polymers6,19579
Water10,827601
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.915, 141.915, 130.226
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-671-

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, 680 molecules

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


Mass: 62.068 Da / Num. of mol.: 73 / 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-XO4 / (5S)-5-butyl-4-({1-[(4-fluorophenyl)methyl]-1H-imidazol-5-yl}methyl)-1-[3-(trifluoromethoxy)phenyl]piperazin-2-one


Mass: 504.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28F4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 3.35 Å3/Da / Density % sol: 63.34 %
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-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.026→46.82 Å / Num. obs: 85639 / % possible obs: 98.92 % / Redundancy: 6 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.07922 / Rpim(I) all: 0.0348 / Rrim(I) all: 0.08676 / Net I/σ(I): 14.46
Reflection shellResolution: 2.026→2.099 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.7557 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 7820 / CC1/2: 0.898 / CC star: 0.973 / Rpim(I) all: 0.3441 / Rrim(I) all: 0.8326 / % possible all: 91.55

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SFX

3sfx


Resolution: 2.026→46.82 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1991 4306 5.05 %
Rwork0.1719 155153 -
obs0.1733 85573 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.55 Å2 / Biso mean: 38.4245 Å2 / Biso min: 18.82 Å2
Refinement stepCycle: final / Resolution: 2.026→46.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6382 0 398 601 7381
Biso mean--46.93 45.55 -
Num. residues----806
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.026-2.04890.32272110.3129382074
2.0489-2.0730.3022920.29965213100
2.073-2.09830.32422270.27115268100
2.0983-2.12490.27162790.25575226100
2.1249-2.15280.25892900.24695220100
2.1528-2.18230.26492670.23755256100
2.1823-2.21350.24752900.23385215100
2.2135-2.24660.25532580.22355198100
2.2466-2.28170.23642720.2255234100
2.2817-2.31910.2562840.21655208100
2.3191-2.35910.23732440.20345253100
2.3591-2.4020.20623120.19555179100
2.402-2.44810.23233020.19655208100
2.4481-2.49810.21022620.18825241100
2.4981-2.55240.20442810.18585207100
2.5524-2.61180.21412760.18865213100
2.6118-2.67710.20892760.17835238100
2.6771-2.74950.20562800.17535234100
2.7495-2.83040.17913160.17245201100
2.8304-2.92170.18922830.16995165100
2.9217-3.02610.21792340.17275287100
3.0261-3.14730.20972670.17255245100
3.1473-3.29050.18573090.16075187100
3.2905-3.46390.21182550.16325278100
3.4639-3.68080.17712690.15455205100
3.6808-3.96490.16682690.13715203100
3.9649-4.36370.17222880.13565229100
4.3637-4.99450.14942850.12895190100
4.9945-6.29010.18973320.1642513399
6.2901-46.820.17742390.1505519998

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