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- PDB-8t70: Cryptococcus neoformans protein farnesyltransferase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8t70
TitleCryptococcus neoformans protein farnesyltransferase in complex with FPTII and TKCMIIM peptide
Components
  • MET-ILE-ILE-MET
  • Protein farnesyltransferase subunit betaFarnesyltransferase
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTRANSFERASE / Protein prenylyltransferase / TRANSFERASE-substrate 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 / benzenethiol / Chem-FII / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / Protein farnesyltransferase subunit beta
Similarity search - Component
Biological speciesCryptococcus neoformans (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsWang, 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: To Be Published
Title: Cryptococcus neoformans protein farnesyltransferase in complex with FPTII and TKCMIIM peptide
Authors: Wang, Y. / Beese, L.S.
History
DepositionJun 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
P: MET-ILE-ILE-MET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,23532
Polymers98,5603
Non-polymers2,67429
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14630 Å2
ΔGint36 kcal/mol
Surface area29500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.768, 140.768, 129.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21B-930-

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


Mass: 40913.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: J9VSJ6
#2: Protein Protein farnesyltransferase subunit beta / Farnesyltransferase


Mass: 56806.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: T2BPA1

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide MET-ILE-ILE-MET


Mass: 840.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 401 molecules

#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: 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
#7: Chemical ChemComp-FII / [(3,7,11-TRIMETHYL-DODECA-2,6,10-TRIENYLOXYCARBAMOYL)-METHYL]-PHOSPHONIC ACID / FPP ANALOG


Mass: 359.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C17H30NO5P / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-BT6 / benzenethiol / Thiophenol


Mass: 110.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6S
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 3.51 Å3/Da / Density % sol: 64.92 %
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: Mar 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.892→49.77 Å / Num. obs: 103014 / % possible obs: 99.25 % / Redundancy: 5.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.052 / Rrim(I) all: 0.129 / Net I/σ(I): 8.08
Reflection shellResolution: 1.892→1.959 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 10141 / CC1/2: 0.931 / Rpim(I) all: 0.306 / Rrim(I) all: 0.755 / % possible all: 98.87

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.892→49.77 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 5171 5.02 %
Rwork0.1849 --
obs0.1861 102952 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.892→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6408 0 169 372 6949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.789
X-RAY DIFFRACTIONf_dihedral_angle_d13.2352479
X-RAY DIFFRACTIONf_chiral_restr0.047969
X-RAY DIFFRACTIONf_plane_restr0.0081171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.892-1.910.32673150.28246180X-RAY DIFFRACTION97
1.91-1.940.32873020.27996219X-RAY DIFFRACTION99
1.94-1.960.31093570.26376243X-RAY DIFFRACTION100
1.96-1.980.28253060.2516251X-RAY DIFFRACTION99
1.98-2.010.28323120.24056298X-RAY DIFFRACTION99
2.01-2.040.29373420.23556201X-RAY DIFFRACTION99
2.04-2.070.27723730.23566218X-RAY DIFFRACTION99
2.07-2.10.25032860.22756299X-RAY DIFFRACTION100
2.1-2.130.24633150.20866266X-RAY DIFFRACTION100
2.13-2.170.24033400.20886274X-RAY DIFFRACTION100
2.17-2.20.2553200.21146028X-RAY DIFFRACTION96
2.2-2.240.22423000.20176118X-RAY DIFFRACTION97
2.24-2.290.22633290.20326267X-RAY DIFFRACTION100
2.29-2.330.24813250.19176303X-RAY DIFFRACTION100
2.33-2.380.20393610.18776188X-RAY DIFFRACTION99
2.38-2.440.22763570.18256227X-RAY DIFFRACTION100
2.44-2.50.22782980.18526327X-RAY DIFFRACTION100
2.5-2.570.20413410.18986223X-RAY DIFFRACTION100
2.57-2.640.23783260.19336251X-RAY DIFFRACTION100
2.64-2.730.22733460.18966299X-RAY DIFFRACTION100
2.73-2.830.21453600.19296211X-RAY DIFFRACTION100
2.83-2.940.19663120.19326308X-RAY DIFFRACTION100
2.94-3.070.20573190.19736272X-RAY DIFFRACTION100
3.07-3.230.20793410.19785940X-RAY DIFFRACTION95
3.23-3.440.2243100.19686295X-RAY DIFFRACTION100
3.44-3.70.21143240.18096293X-RAY DIFFRACTION100
3.7-4.070.19533400.1626228X-RAY DIFFRACTION100
4.07-4.660.16573380.14646252X-RAY DIFFRACTION100
4.66-5.870.1963880.15576134X-RAY DIFFRACTION99
5.87-49.770.16362750.15076007X-RAY DIFFRACTION95

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