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- PDB-7t0a: Cryptococcus neoformans protein farnesyltransferase co-crystalliz... -

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Basic information

Entry
Database: PDB / ID: 7t0a
TitleCryptococcus neoformans protein farnesyltransferase co-crystallized with FPP and inhibitor 2f
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 / Chem-XMY / 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: 2.099 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

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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)102,82167
Polymers97,7202
Non-polymers5,10165
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20220 Å2
ΔGint132 kcal/mol
Surface area29850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.210, 141.210, 129.822
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-620-

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, 486 molecules

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


Mass: 62.068 Da / Num. of mol.: 59 / 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-XMY / (5S)-4-({1-[(4-bromophenyl)methyl]-1H-imidazol-5-yl}methyl)-5-butyl-1-[3-(trifluoromethoxy)phenyl]piperazin-2-one


Mass: 565.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28BrF3N4O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 3.31 Å3/Da / Density % sol: 62.86 %
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: 2.099→49.93 Å / Num. obs: 76837 / % possible obs: 99.71 % / Redundancy: 6.2 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08403 / Rpim(I) all: 0.03654 / Rrim(I) all: 0.09181 / Net I/σ(I): 14.54
Reflection shellResolution: 2.099→2.174 Å / Redundancy: 6 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 7492 / CC1/2: 0.872 / CC star: 0.965 / Rpim(I) all: 0.3423 / Rrim(I) all: 0.8461 / % possible all: 98.21

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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: 2.099→49.93 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2126 1997 2.59 %
Rwork0.1867 142456 -
obs0.1873 76837 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.33 Å2 / Biso mean: 41.124 Å2 / Biso min: 17.16 Å2
Refinement stepCycle: final / Resolution: 2.099→49.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6375 0 323 421 7119
Biso mean--51.83 47.33 -
Num. residues----804
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.099-2.130.28821290.303504895
2.13-2.150.36971210.28255275100
2.15-2.180.29791520.27135276100
2.18-2.210.30431480.26285274100
2.21-2.250.24331380.25465319100
2.25-2.280.29991360.255214100
2.28-2.320.25751370.23675341100
2.32-2.360.2651430.22935265100
2.36-2.40.2551570.22165281100
2.4-2.450.24251410.21555265100
2.45-2.50.22131340.21535271100
2.5-2.550.26311380.21085290100
2.55-2.610.21951530.19835291100
2.61-2.680.18421080.20885316100
2.68-2.750.25771690.19875263100
2.75-2.830.21691380.19595276100
2.83-2.920.21451440.18765289100
2.92-3.030.27671250.18875295100
3.03-3.150.20411490.18345316100
3.15-3.290.18011350.18225261100
3.29-3.460.19821530.17465283100
3.46-3.680.20761260.1695314100
3.68-3.970.16851570.15655249100
3.97-4.360.15091440.15255310100
4.36-50.17781430.15075281100
5-6.290.24571380.18175304100
6.29-49.930.20581350.16535289100

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