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- PDB-1qbq: STRUCTURE OF RAT FARNESYL PROTEIN TRANSFERASE COMPLEXED WITH A CV... -

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Basic information

Entry
Database: PDB / ID: 1qbq
TitleSTRUCTURE OF RAT FARNESYL PROTEIN TRANSFERASE COMPLEXED WITH A CVIM PEPTIDE AND ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID.
Components
  • ACETYL-CYS-VAL-ILE-SELENOMET-COOH PEPTIDE
  • FPT ALPHA-SUBUNIT
  • FPT BETA-SUBUNIT
KeywordsTRANSFERASE / ALPHA-ALPHA-BARREL HELICAL CRESCENT
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / regulation of fibroblast proliferation / regulation of microtubule-based movement / geranylgeranyl diphosphate synthase activity / positive regulation of skeletal muscle acetylcholine-gated channel clustering / acetyltransferase activator activity / microtubule associated complex / enzyme-linked receptor protein signaling pathway / positive regulation of Rac protein signal transduction / alpha-tubulin binding / positive regulation of cell cycle / wound healing / receptor tyrosine kinase binding / lipid metabolic process / positive regulation of fibroblast proliferation / fibroblast proliferation / microtubule binding / molecular adaptor activity / cell population proliferation / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / enzyme binding / 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
ACETATE ION / ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID / Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsStrickland, C.L. / Windsor, W.T. / Syto, R. / Wang, L. / Bond, R. / Wu, Z. / Schwartz, J. / Le, H.V. / Beese, L.S. / Weber, P.C.
Citation
Journal: Biochemistry / Year: 1998
Title: Crystal structure of farnesyl protein transferase complexed with a CaaX peptide and farnesyl diphosphate analogue
Authors: Strickland, C.L. / Windsor, W.T. / Syto, R. / Wang, L. / Bond, R. / Wu, Z. / Schwartz, J. / Le, H.V. / Beese, L.S. / Weber, P.C.
#1: Journal: Protein Eng. / Year: 1999
Title: Engineering of protein farnesyl transferase for co-crystallization. Expression, purification and kinetic characterization of Beta-subunit C-terminal mutants.
Authors: Wu, Z. / Demma, M. / Strickland, C.L. / Syto, R. / Le, H.V. / Weber, P.C. / Windsor, W.T.
History
DepositionApr 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _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.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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FPT ALPHA-SUBUNIT
B: FPT BETA-SUBUNIT
P: ACETYL-CYS-VAL-ILE-SELENOMET-COOH PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4536
Polymers89,0203
Non-polymers4333
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-71 kcal/mol
Surface area27160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.132, 174.132, 69.705
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein FPT ALPHA-SUBUNIT


Mass: 39760.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ALPHA AND BETA SUBUNITS FORM THE BIOLOGICAL UNIT / Source: (gene. exp.) Rattus norvegicus (Norway rat)
References: UniProt: Q04631, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Protein FPT BETA-SUBUNIT


Mass: 48722.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
References: UniProt: Q02293, Transferases; Transferring alkyl or aryl groups, other than methyl groups

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide ACETYL-CYS-VAL-ILE-SELENOMET-COOH PEPTIDE


Mass: 537.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Purchased from AnaSpec Inc.

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Non-polymers , 4 types, 287 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Details: Purchased from Calbiochem.
#6: Chemical ChemComp-HFP / ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID


Mass: 308.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H33O4P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.43 Å3/Da / Density % sol: 64.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 7% PEG 4000, 0.1 M sodium acetate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris1drop
21 mMdithiothreitol1drop
320 mM1dropKCl
40.010 mM1dropZnCl2
525 mg/mlprotain1drop
67 %PEG40001reservoir
70.1 Msodium acetate1reservoir
8200 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 6, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. all: 47488 / Num. obs: 42739 / % possible obs: 90 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 44.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3 % / Rmerge(I) obs: 0.371 / Num. unique all: 47488 / % possible all: 57
Reflection
*PLUS
% possible obs: 90 % / Num. measured all: 144714
Reflection shell
*PLUS
% possible obs: 57 % / Mean I/σ(I) obs: 3

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Processing

Software
NameClassification
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→15 Å / σ(F): 0.5 / σ(I): 1
RfactorNum. reflection% reflection
Rfree0.292 1999 5 %
Rwork0.218 --
all-47488 -
obs-40344 -
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5846 0 24 284 6154
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 15 Å / σ(F): 0.5 / % reflection Rfree: 5 % / Rfactor obs: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS

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