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- PDB-2zev: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 2zev
TitleS. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium, IPP and BPH-715
ComponentsGeranylgeranyl pyrophosphate synthetase
KeywordsTRANSFERASE / PRENYLTRANSFERASE / FARNESYL PYROPHOSPHATE / BISPHOSPHONATE / Carotenoid biosynthesis / Isoprene biosynthesis / Multifunctional enzyme / Protein transport / Transport
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
3-(DECYLOXY)-1-(2,2-DIPHOSPHONOETHYL)PYRIDINIUM / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Geranylgeranyl pyrophosphate synthase BTS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsGuo, R.T. / Chen, C.K.-M. / Cao, R. / Oldfield, E. / Wang, A.H.-J.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation
Authors: Zhang, Y. / Cao, R. / Yin, F. / Hudock, M.P. / Guo, R.T. / Krysiak, K. / Mukherjee, S. / Gao, Y.-G. / Robinson, H. / Song, Y. / No, J.H. / Bergan, K. / Leon, A. / Cass, L. / Goddard, A. / ...Authors: Zhang, Y. / Cao, R. / Yin, F. / Hudock, M.P. / Guo, R.T. / Krysiak, K. / Mukherjee, S. / Gao, Y.-G. / Robinson, H. / Song, Y. / No, J.H. / Bergan, K. / Leon, A. / Cass, L. / Goddard, A. / Chang, T.-K. / Lin, F.-Y. / Van Beek, E. / Papapoulos, S. / Wang, A.H.-J. / Kubo, T. / Ochi, M. / Mukkamala, D. / Oldfield, E.
History
DepositionDec 17, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geranylgeranyl pyrophosphate synthetase
B: Geranylgeranyl pyrophosphate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7909
Polymers78,5982
Non-polymers1,1927
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9600 Å2
ΔGint-100 kcal/mol
Surface area24790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.822, 115.879, 128.336
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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q12051, heptaprenyl diphosphate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-B71 / 3-(DECYLOXY)-1-(2,2-DIPHOSPHONOETHYL)PYRIDINIUM / 2-(3-DECYLOXY-PYRIDINUM-1-YL)-1,1-BISPHOSPHONIC ACID


Mass: 424.386 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H32NO7P2
#4: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
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 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / 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: 2.23→50 Å / Num. all: 35636 / Num. obs: 33587 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 41.3
Reflection shellResolution: 2.23→2.31 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3069 / % possible all: 86.6

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Processing

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

2dh4


Resolution: 2.23→41.81 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1605 -RANDOM
Rwork0.2 ---
obs0.2 32352 90.8 %-
all-35636 --
Displacement parametersBiso mean: 48.64 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati sigma a obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.23→41.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4879 0 72 452 5403
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.7
LS refinement shellResolution: 2.23→2.31 Å
RfactorNum. reflection
Rfree0.333 134
Rwork0.266 -
obs-2793

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