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- PDB-4l9p: Crystal structure of Aspergillus fumigatus protein farnesyltransf... -

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Basic information

Entry
Database: PDB / ID: 4l9p
TitleCrystal structure of Aspergillus fumigatus protein farnesyltransferase complexed with the FII analog, FPT-II, and the KCVVM peptide
Components
  • (CaaX farnesyltransferase ...) x 2
  • LYS-CYS-VAL-VAL-MET (CAAX peptide)
KeywordsTRANSFERASE / Ternary complex with isoprenoid and CAAX peptide substrate / CAAX farnesyltransferase / Isoprenoid and CAAX protein/peptide substrate
Function / homology
Function and homology information


prenylation / peptide pheromone maturation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / zinc ion binding / cytoplasm
Similarity search - Function
Protein farnesyltransferase subunit beta / Protein prenylyltransferase / 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 / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid ...Protein farnesyltransferase subunit beta / Protein prenylyltransferase / 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 / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Chem-FII / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / Protein farnesyltransferase subunit beta
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMabanglo, M.F. / Hast, M.A. / Beese, L.S.
CitationJournal: Protein Sci. / Year: 2014
Title: Crystal structures of the fungal pathogen Aspergillus fumigatus protein farnesyltransferase complexed with substrates and inhibitors reveal features for antifungal drug design.
Authors: Mabanglo, M.F. / Hast, M.A. / Lubock, N.B. / Hellinga, H.W. / Beese, L.S.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CaaX farnesyltransferase alpha subunit Ram2
B: CaaX farnesyltransferase beta subunit Ram1
C: LYS-CYS-VAL-VAL-MET (CAAX peptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,69717
Polymers99,6073
Non-polymers1,09014
Water14,016778
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11870 Å2
ΔGint-72 kcal/mol
Surface area28840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.236, 90.328, 83.007
Angle α, β, γ (deg.)90.00, 111.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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CaaX farnesyltransferase ... , 2 types, 2 molecules AB

#1: Protein CaaX farnesyltransferase alpha subunit Ram2


Mass: 42391.461 Da / Num. of mol.: 1 / Mutation: N146S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: Af293 / Gene: AFUA_4G07800 / Plasmid: pCDF-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: Q4WP27, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Protein CaaX farnesyltransferase beta subunit Ram1


Mass: 56635.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: Af293 / Gene: AFUA_4G10330 / Plasmid: pCDF-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q4WPS9, protein farnesyltransferase

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide LYS-CYS-VAL-VAL-MET (CAAX peptide)


Mass: 579.795 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 5 types, 792 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#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: obtained synthetically / Formula: C17H30NO5P
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 778 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4-10% PEG6000, 600-800 mM LiCl, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2012
RadiationMonochromator: Double-crystal, liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 156214 / Num. obs: 154808 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 36
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 2 / % possible all: 82.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: > Homology model of A. fumigatus farnesyltransferase generated using PHYRE

Resolution: 1.45→22.421 Å / SU ML: 0.12 / σ(F): 1.33 / Phase error: 13.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.152 7183 5.02 %Random
Rwork0.1251 ---
obs0.1264 153441 98.86 %-
all-154808 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→22.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6273 0 64 778 7115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0196788
X-RAY DIFFRACTIONf_angle_d1.8339251
X-RAY DIFFRACTIONf_dihedral_angle_d13.8752521
X-RAY DIFFRACTIONf_chiral_restr0.137966
X-RAY DIFFRACTIONf_plane_restr0.0111212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4458-1.46220.25882310.20994106X-RAY DIFFRACTION84
1.4622-1.47940.22632310.18944671X-RAY DIFFRACTION94
1.4794-1.49740.20992280.17434741X-RAY DIFFRACTION97
1.4974-1.51640.2422800.19554750X-RAY DIFFRACTION98
1.5164-1.53630.21172600.16864924X-RAY DIFFRACTION99
1.5363-1.55740.18162410.14594866X-RAY DIFFRACTION100
1.5574-1.57960.18392580.12454887X-RAY DIFFRACTION100
1.5796-1.60320.14722590.11494882X-RAY DIFFRACTION100
1.6032-1.62820.14622720.10814908X-RAY DIFFRACTION100
1.6282-1.65490.15732720.11124846X-RAY DIFFRACTION100
1.6549-1.68350.16352920.1124835X-RAY DIFFRACTION100
1.6835-1.71410.14812720.11354903X-RAY DIFFRACTION100
1.7141-1.7470.16272520.12094914X-RAY DIFFRACTION100
1.747-1.78270.14342460.10874883X-RAY DIFFRACTION99
1.7827-1.82140.15032790.10834843X-RAY DIFFRACTION99
1.8214-1.86380.14192580.10114898X-RAY DIFFRACTION100
1.8638-1.91030.14852860.09944858X-RAY DIFFRACTION99
1.9103-1.9620.13742600.10284867X-RAY DIFFRACTION99
1.962-2.01970.14412650.10584869X-RAY DIFFRACTION100
2.0197-2.08480.12952610.09884857X-RAY DIFFRACTION100
2.0848-2.15930.14682600.10074924X-RAY DIFFRACTION100
2.1593-2.24560.12912570.10384895X-RAY DIFFRACTION100
2.2456-2.34770.14192840.11064887X-RAY DIFFRACTION100
2.3477-2.47140.15062350.11464927X-RAY DIFFRACTION100
2.4714-2.6260.14462590.12364948X-RAY DIFFRACTION100
2.626-2.82840.15072170.12944929X-RAY DIFFRACTION100
2.8284-3.11230.15772430.13454954X-RAY DIFFRACTION100
3.1123-3.56120.16482710.13714944X-RAY DIFFRACTION100
3.5612-4.48080.12582410.12874970X-RAY DIFFRACTION100
4.4808-22.42420.15622380.14895047X-RAY DIFFRACTION100

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