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- PDB-4lng: Aspergillus fumigatus protein farnesyltransferase complex with fa... -

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Basic information

Entry
Database: PDB / ID: 4lng
TitleAspergillus fumigatus protein farnesyltransferase complex with farnesyldiphosphate and tipifarnib
Components(CaaX farnesyltransferase ...) x 2
KeywordsTRANSFERASE / Farnesyltransferase / Prenylation / Isoprenoid and CAAX-containing protein and peptide substrates / Farnesylation
Function / homology
Function and homology information


peptide pheromone maturation / prenylation / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / 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 and squalene oxidase repeat / 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 and squalene oxidase repeat / 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 / Chem-JAN / : / 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: 1.905 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
DepositionJul 11, 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)100,31411
Polymers99,0272
Non-polymers1,2879
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-87 kcal/mol
Surface area29360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.537, 90.658, 83.163
Angle α, β, γ (deg.)90.00, 111.09, 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
Fragment: Aspergillus fumigatus protein farnesyltransferase alpha subunit
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, NCBI Locus XM_746952 Ram2 gene / Plasmid: pCDFDuet 1 / 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
Fragment: Aspergillus fumigatus protein farnesyltransferase beta subunit
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, NCBI Locus XM_746700 Ram1 gene / Plasmid: pCDF Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q4WPS9, protein farnesyltransferase

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Non-polymers , 6 types, 604 molecules

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


Mass: 62.068 Da / Num. of mol.: 5 / 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-JAN / 6-[(S)-AMINO(4-CHLOROPHENYL)(1-METHYL-1H-IMIDAZOL-5-YL)METHYL]-4-(3-CHLOROPHENYL)-1-METHYLQUINOLIN-2(1H)-ONE / R115777 / TIPIFARNIB / Tipifarnib


Mass: 489.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H22Cl2N4O / Comment: inhibitor*YM
#6: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE / Farnesyl pyrophosphate


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#7: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growMethod: 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

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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: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 68148 / Num. obs: 66308 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.905→30.237 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 17.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 3239 4.89 %
Rwork0.1548 --
obs0.1563 66203 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.905→30.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6192 0 80 595 6867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036643
X-RAY DIFFRACTIONf_angle_d0.7939067
X-RAY DIFFRACTIONf_dihedral_angle_d11.8932457
X-RAY DIFFRACTIONf_chiral_restr0.061947
X-RAY DIFFRACTIONf_plane_restr0.0031188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9054-1.93380.247850.2211766X-RAY DIFFRACTION62
1.9338-1.9640.231380.21062379X-RAY DIFFRACTION85
1.964-1.99620.2321260.19942509X-RAY DIFFRACTION89
1.9962-2.03060.25071560.18832560X-RAY DIFFRACTION92
2.0306-2.06760.21141390.18882701X-RAY DIFFRACTION95
2.0676-2.10730.22221490.17582750X-RAY DIFFRACTION97
2.1073-2.15030.20271580.17042729X-RAY DIFFRACTION99
2.1503-2.19710.18021480.16172843X-RAY DIFFRACTION99
2.1971-2.24820.19691380.15842838X-RAY DIFFRACTION100
2.2482-2.30440.20841630.15822808X-RAY DIFFRACTION100
2.3044-2.36660.18141650.15242810X-RAY DIFFRACTION100
2.3666-2.43620.2171260.15172856X-RAY DIFFRACTION100
2.4362-2.51480.18131350.1462831X-RAY DIFFRACTION100
2.5148-2.60470.17531480.15692820X-RAY DIFFRACTION100
2.6047-2.70890.21831260.15342868X-RAY DIFFRACTION100
2.7089-2.83210.20111420.15262835X-RAY DIFFRACTION100
2.8321-2.98130.18021410.15932826X-RAY DIFFRACTION100
2.9813-3.16790.18911350.1512885X-RAY DIFFRACTION100
3.1679-3.41220.1631610.14792809X-RAY DIFFRACTION100
3.4122-3.7550.17851450.13992882X-RAY DIFFRACTION100
3.755-4.2970.14431450.12882837X-RAY DIFFRACTION100
4.297-5.40870.13991320.14132892X-RAY DIFFRACTION100
5.4087-30.24070.1871380.16192930X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 25.1798 Å / Origin y: -9.6615 Å / Origin z: 9.2197 Å
111213212223313233
T0.1018 Å20.0063 Å2-0.0158 Å2-0.0913 Å20.0062 Å2--0.1083 Å2
L0.6936 °20.0318 °2-0.0545 °2-0.6619 °20.1022 °2--0.5331 °2
S-0.0051 Å °-0.0146 Å °0.004 Å °-0.0331 Å °-0.0103 Å °0.0321 Å °0.03 Å °-0.0245 Å °0.0078 Å °
Refinement TLS groupSelection details: all

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