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- PDB-1ft1: CRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE AT 2.25 ANGSTROM... -

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Basic information

Entry
Database: PDB / ID: 1ft1
TitleCRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE AT 2.25 ANGSTROMS RESOLUTION
Components(PROTEIN FARNESYLTRANSFERASE) x 2
KeywordsTRANSFERASE / CANCER THERAPEUTICS / G PROTEINS / PRENYLTRANSFERASE / SIGNAL TRANSDUCTION / RAS
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / protein geranylgeranyltransferase type I / positive regulation of tubulin deacetylation / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / protein geranylgeranyltransferase type I / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / regulation of fibroblast proliferation / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / negative regulation of nitric-oxide synthase biosynthetic process / farnesyltranstransferase activity / microtubule associated complex / enzyme-linked receptor protein signaling pathway / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of Rac protein signal transduction / alpha-tubulin binding / positive regulation of cell cycle / response to cytokine / wound healing / lipid metabolic process / response to organic cyclic compound / receptor tyrosine kinase binding / positive regulation of fibroblast proliferation / fibroblast proliferation / microtubule binding / cell population proliferation / molecular adaptor activity / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / 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
Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.25 Å
AuthorsBeese, L.S. / Park, H.-W.
Citation
Journal: Science / Year: 1997
Title: Crystal structure of protein farnesyltransferase at 2.25 angstrom resolution.
Authors: Park, H.W. / Boduluri, S.R. / Moomaw, J.F. / Casey, P.J. / Beese, L.S.
#1: Journal: Science / Year: 1997
Title: Erratum. Crystal Structure of Protein Farnesyltransferase at 2.25 Angstrom Resolution
Authors: Park, H.W. / Boduluri, S.R. / Moomaw, J.F. / Casey, P.J. / Beese, L.S.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: High Level Expression of Mammalian Protein Farnesyltransferase in a Baculovirus System. The Purified Protein Contains Zinc
Authors: Chen, W.J. / Moomaw, J.F. / Overton, L. / Kost, T.A. / Casey, P.J.
History
DepositionMar 17, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN FARNESYLTRANSFERASE
B: PROTEIN FARNESYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8863
Polymers92,8202
Non-polymers651
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-49 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.060, 167.060, 97.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PROTEIN FARNESYLTRANSFERASE


Mass: 44098.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: CYTOPLASM / Gene: CDNA / Organ: BRAIN / Plasmid: BACULOVIRUS / Cell line (production host): SF9 / Cellular location (production host): CYTOPLASM / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04631, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Protein PROTEIN FARNESYLTRANSFERASE


Mass: 48722.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: CYTOPLASM / Gene: CDNA / Organ: BRAIN / Plasmid: BACULOVIRUS / Cell line (production host): SF9 / Cellular location (production host): CYTOPLASM / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q02293, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 402 / 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: 3.79 Å3/Da / Density % sol: 68 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANG DROP, PROTEIN CONCENTRATION BETWEEN 4 AND 16MG/ML IN 20 MM KCL, 10MM ZNCL, 10MM DTT, 20MM TRIS PH7.7, RESERVOIR SOLUTION OF 13 - 18% PEG 8000, 200MM AMMONIUM ACETATE, PH 7.0, vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14-16 mg/mlFTase1drop
220 mM1dropKCl
310 mM1dropZnCl
410 mMdithiothreitol1drop
520 mMTris-HCl1drop
613-15 %(w/v)PEG80001drop
7200 mMammonium acetate1drop
813-15 %(w/v)PEG80001reservoir
9200 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 17, 1997 / Details: MSC DOUBLE-MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. obs: 72290 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 18.4
Reflection shellResolution: 2.25→2.28 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 0.92 / Rsym value: 0.556 / % possible all: 81.8
Reflection
*PLUS
Num. measured all: 442035

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 2.25→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2825 4.52 %YES
Rwork0.21 ---
obs0.21 62497 89.58 %-
Displacement parametersBiso mean: 31.2 Å2
Refine analyzeLuzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.25→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5950 0 1 403 6354
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.748
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.43
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.364
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.4541.5
X-RAY DIFFRACTIONx_mcangle_it1.1322
X-RAY DIFFRACTIONx_scbond_it1.4542
X-RAY DIFFRACTIONx_scangle_it1.1322.5
LS refinement shellResolution: 2.25→2.35 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.35 281 3.23 %
Rwork0.36 5298 -
obs--64.16 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.436
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.364

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