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

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Basic information

Entry
Database: PDB / ID: 4mbg
TitleCrystal structure of Aspergillus fumigatus protein farnesyltransferase binary complex with farnesyldiphosphate
Components(CaaX farnesyltransferase ...) x 2
KeywordsTRANSFERASE / farnesyldiphosphate / farnesyltransferase inhibitor
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
FARNESYL DIPHOSPHATE / : / 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: 1.74 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
DepositionAug 19, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,88711
Polymers99,0272
Non-polymers8599
Water12,611700
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9600 Å2
ΔGint-54 kcal/mol
Surface area29600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.252, 90.793, 83.138
Angle α, β, γ (deg.)90.00, 110.87, 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: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_4G07800 / Plasmid: pCDF Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41
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: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_4G10330 / Plasmid: pCDF Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q4WPS9, protein farnesyltransferase

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Non-polymers , 5 types, 709 molecules

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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 290 K / pH: 7.5
Details: 4-10 % PEG6000, 600-800 mM LiCl, and 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: 0.97
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: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 89198 / % possible obs: 99.8 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data 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 ASPERGILLUS FUMIGATUS PROTEIN FARNESYLTRANSFERASE GENERATED USING PHYRE

Resolution: 1.74→23.96 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 14.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.164 4422 4.96 %
Rwork0.122 --
obs0.124 89162 99.4 %
all-89377 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→23.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6185 0 50 700 6935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116631
X-RAY DIFFRACTIONf_angle_d1.2319058
X-RAY DIFFRACTIONf_dihedral_angle_d13.5622461
X-RAY DIFFRACTIONf_chiral_restr0.089947
X-RAY DIFFRACTIONf_plane_restr0.0061186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7417-1.76150.28641180.21992420X-RAY DIFFRACTION84
1.7615-1.78220.19691340.19172815X-RAY DIFFRACTION99
1.7822-1.8040.22321660.17072822X-RAY DIFFRACTION100
1.804-1.82680.20181710.14972753X-RAY DIFFRACTION100
1.8268-1.85080.18881520.1322865X-RAY DIFFRACTION100
1.8508-1.87620.17611460.11522842X-RAY DIFFRACTION100
1.8762-1.9030.17581690.11362764X-RAY DIFFRACTION100
1.903-1.93140.16181400.12182849X-RAY DIFFRACTION100
1.9314-1.96150.18261560.13182816X-RAY DIFFRACTION100
1.9615-1.99370.18541480.14222810X-RAY DIFFRACTION100
1.9937-2.0280.18451680.10962834X-RAY DIFFRACTION100
2.028-2.06490.17771390.10282832X-RAY DIFFRACTION100
2.0649-2.10460.15121570.10482843X-RAY DIFFRACTION100
2.1046-2.14750.14761560.10052774X-RAY DIFFRACTION100
2.1475-2.19420.14781530.10012880X-RAY DIFFRACTION100
2.1942-2.24520.14361360.1092832X-RAY DIFFRACTION100
2.2452-2.30130.18021650.10622817X-RAY DIFFRACTION100
2.3013-2.36350.15611640.10632838X-RAY DIFFRACTION100
2.3635-2.43290.16621280.11022871X-RAY DIFFRACTION100
2.4329-2.51140.16411390.1072819X-RAY DIFFRACTION100
2.5114-2.6010.14721470.11232847X-RAY DIFFRACTION100
2.601-2.7050.16461280.11292857X-RAY DIFFRACTION100
2.705-2.8280.15181390.11772861X-RAY DIFFRACTION100
2.828-2.97680.15631430.12452831X-RAY DIFFRACTION100
2.9768-3.16290.1641390.12742895X-RAY DIFFRACTION100
3.1629-3.40650.15771520.1292803X-RAY DIFFRACTION100
3.4065-3.74820.17021520.12542870X-RAY DIFFRACTION100
3.7482-4.28780.15251460.12042867X-RAY DIFFRACTION100
4.2878-5.3920.14321300.1162897X-RAY DIFFRACTION100
5.392-23.95910.16731410.1442916X-RAY DIFFRACTION100

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