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- PDB-2e93: S. cerevisiae geranylgeranyl pyrophosphate synthase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 2.0E+93
TitleS. cerevisiae geranylgeranyl pyrophosphate synthase in complex with BPH-629
ComponentsGeranylgeranyl pyrophosphate synthetase
KeywordsTRANSFERASE / prenyltransferase / farnesyl pyrophosphate / bisphosphonate
Function / homology
Function and homology information


Cholesterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / geranyl diphosphate biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranylgeranyl diphosphate synthase activity / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / terpenoid biosynthetic process / isoprenoid biosynthetic process ...Cholesterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / geranyl diphosphate biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranylgeranyl diphosphate synthase activity / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / terpenoid biosynthetic process / isoprenoid biosynthetic process / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / protein transport / mitochondrion / metal ion binding
Similarity search - Function
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-B29 / Geranylgeranyl pyrophosphate synthase BTS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsGuo, R.T. / Cao, R. / Ko, T.P. / Chen, C.K.-M. / Jeng, W.Y. / Chang, T.H. / Liang, P.H. / Oldfield, E. / Wang, A.H.-J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases
Authors: Guo, R.T. / Cao, R. / Liang, P.H. / Ko, T.P. / Chang, T.H. / Hudock, M.P. / Jeng, W.Y. / Chen, C.K.-M. / Zhang, Y. / Song, Y. / Kuo, C.J. / Yin, F. / Oldfield, E. / Wang, A.H.-J.
History
DepositionJan 24, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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: Geranylgeranyl pyrophosphate synthetase
B: Geranylgeranyl pyrophosphate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3916
Polymers78,5982
Non-polymers1,7934
Water9,350519
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-67 kcal/mol
Surface area25260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.788, 115.821, 129.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Geranylgeranyl pyrophosphate synthetase / GGPP synthetase / GGPPSase / Geranylgeranyl diphosphate synthase / BET2 suppressor protein 1


Mass: 39299.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET32/LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q12051, heptaprenyl diphosphate synthase
#2: Chemical
ChemComp-B29 / [2-(3-DIBENZOFURAN-4-YL-PHENYL)-1-HYDROXY-1-PHOSPHONO-ETHYL]-PHOSPHONIC ACID / [2-(3-DIBENZO[B,D]FURAN-4-YLPHENYL)-1-HYDROXYETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)


Mass: 448.300 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H18O8P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.08M CH3COONa, 16% PEG 4000, 6-10% glycerol, 6-10% 1,2-propanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. all: 40139 / Num. obs: 38573 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Redundancy: 4.52 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 28.7
Reflection shellResolution: 2.12→2.2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3357 / % possible all: 85.2

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DH4

2dh4


Resolution: 2.12→28.96 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1873 -RANDOM
Rwork0.167 ---
all-40139 --
obs-37579 93.6 %-
Displacement parametersBiso mean: 36.57 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å / Luzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 2.12→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5013 0 120 519 5652
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.7
LS refinement shellResolution: 2.12→2.2 Å
RfactorNum. reflection
Rfree0.242 151
Rwork0.181 -
obs-2907

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