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- PDB-3dra: Candida albicans protein geranylgeranyltransferase-I complexed wi... -

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Basic information

Entry
Database: PDB / ID: 3dra
TitleCandida albicans protein geranylgeranyltransferase-I complexed with GGPP
Components
  • Geranylgeranyltransferase type I beta subunit
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTRANSFERASE / geranylgeranyltrasferase / geranylgeranyltransferase type-I / GGTase / GGTase-I / PGGT / prenyltransferase / farnesyltransferase / prenylation / geranylgeranylpyrophosphate / GGPP / geranylgeranyl diphosphate / Candida / Candida albicans
Function / homology
Function and homology information


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 / protein geranylgeranylation
Similarity search - Function
Protein prenylyltransferase / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / Glycosyltransferase - #20 / Glycosyltransferase / Alpha/alpha barrel / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
GERANYLGERANYL DIPHOSPHATE / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHast, M.A. / Beese, L.S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure of protein geranylgeranyltransferase-I from the human pathogen Candida albicans complexed with a lipid substrate.
Authors: Hast, M.A. / Beese, L.S.
History
DepositionJul 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Geranylgeranyltransferase type I beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1235
Polymers82,3252
Non-polymers7983
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-33 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.304, 66.049, 82.821
Angle α, β, γ (deg.)90.00, 100.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / CAAX farnesyltransferase subunit alpha / Ras proteins prenyltransferase alpha / FTase-alpha / Type ...CAAX farnesyltransferase subunit alpha / Ras proteins prenyltransferase alpha / FTase-alpha / Type I protein geranyl-geranyltransferase subunit alpha / GGTase-I-alpha


Mass: 36659.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: RAM2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y765, protein farnesyltransferase, protein geranylgeranyltransferase type I
#2: Protein Geranylgeranyltransferase type I beta subunit


Mass: 45665.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: CDC43 / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 474 molecules

#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE


Mass: 450.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H36O7P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsACCORDING TO THE AUTHORS THE GENES FOR THE SUBUNITS OF THE ENZYME FROM THIS ORGANISM EXHIBIT ...ACCORDING TO THE AUTHORS THE GENES FOR THE SUBUNITS OF THE ENZYME FROM THIS ORGANISM EXHIBIT SIGNIFICANT VARIATION ACROSS STRAINS AND EVEN ALLELES. THE UNIPROT ENTRIES DO NOT MATCH ALL OBSERVATIONS OF SEQUENCE VARIATION FOR THESE GENES IN THE LITERATURE.

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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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 1500, propionate-cacodylate-bis-tris buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 63895 / % possible obs: 98.17 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.85 Å / % possible all: 76.8

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→37.64 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.008 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 3.1 / σ(I): -3 / ESU R: 0.145 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23056 3226 5 %RANDOM
Rwork0.19201 ---
all0.19398 63895 --
obs0.19398 60658 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.285 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5582 0 49 471 6102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225764
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.9557800
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0545662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94825.016307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.449151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9451522
X-RAY DIFFRACTIONr_chiral_restr0.0830.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214384
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7411.53324
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42825393
X-RAY DIFFRACTIONr_scbond_it2.21332440
X-RAY DIFFRACTIONr_scangle_it3.5994.52407
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 206 -
Rwork0.256 3441 -
obs--76.8 %

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