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- PDB-2z4y: S. cerevisiae geranylgeranyl pyrophosphate synthase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 2z4y
TitleS. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and BPH-252
ComponentsGeranylgeranyl pyrophosphate synthetase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / prenyltransferase / geranylgeranyl pyrophosphate / bisphosphonate / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Cholesterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / farnesyltranstransferase activity ...Cholesterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / farnesyltranstransferase activity / geranyltranstransferase activity / terpenoid biosynthetic process / prenyltransferase activity / isoprenoid biosynthetic process / 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
(1-HYDROXYNONANE-1,1-DIYL)BIS(PHOSPHONIC ACID) / Geranylgeranyl pyrophosphate synthase BTS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, C.K.-M. / Guo, R.T. / Hudock, M. / Cao, R. / Oldfield, E. / Wang, A.H.-J.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates: a crystallographic and computational investigation
Authors: Chen, C.K.-M. / Hudock, M.P. / Zhang, Y. / Guo, R.-T. / Cao, R. / No, J.H. / Liang, P.-H. / Ko, T.-P. / Chang, T.-H. / Chang, S.-C. / Song, Y. / Axelson, J. / Kumar, A. / Wang, A.H.-J. / Oldfield, E.
History
DepositionJun 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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)79,5356
Polymers78,5982
Non-polymers9374
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-67 kcal/mol
Surface area23990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.952, 116.208, 126.020
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 Xa/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q12051, heptaprenyl diphosphate synthase, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase, geranylgeranyl diphosphate synthase
#2: Chemical ChemComp-252 / (1-HYDROXYNONANE-1,1-DIYL)BIS(PHOSPHONIC ACID)


Mass: 304.214 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H22O7P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
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 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 23, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 40284 / Num. obs: 40023 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 29.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3951 / % possible all: 99.7

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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: 2.1→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1942 -RANDOM
Rwork0.181 ---
all-40284 --
obs-38785 96.3 %-
Displacement parametersBiso mean: 38.27 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4663 0 55 391 5109
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.7
LS refinement shellResolution: 2.1→2.18 Å
RfactorNum. reflection% reflection
Rfree0.256 199 -
Rwork0.197 --
obs-3538 89.5 %

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