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- PDB-2f6x: Crystal Structure of (S)-3-O-Geranylgeranylglyceryl Phosphate Syn... -

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Basic information

Entry
Database: PDB / ID: 2f6x
TitleCrystal Structure of (S)-3-O-Geranylgeranylglyceryl Phosphate Synthase complexed with sn-G1P and MPD
Components(S)-3-O-Geranylgeranylglyceryl Phosphate Synthase
KeywordsTRANSFERASE / non-canonical TIM-barrel / prenyltransferase / archaeal lipid synthesis / sn-glycerol-1-phosphate / 2-methyl-2 / 4-pentanediol / dimer
Function / homology
Function and homology information


phosphoglycerol geranylgeranyltransferase / phosphoglycerol geranylgeranyltransferase activity / glycerophospholipid biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
Geranylgeranylglyceryl phosphate synthase, archaea / GGGP/HepGP synthase group I / FMN-linked oxidoreductases / Geranylgeranylglyceryl phosphate synthase/Heptaprenylglyceryl phosphate synthase / GGGP/HepGP synthase superfamily / PcrB family / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
SN-GLYCEROL-1-PHOSPHATE / Geranylgeranylglyceryl phosphate synthase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPayandeh, J.M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase reveals an ancient fold for an ancient enzyme
Authors: Payandeh, J. / Fujihashi, M. / Gillon, W. / Pai, E.F.
History
DepositionNov 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (S)-3-O-Geranylgeranylglyceryl Phosphate Synthase
B: (S)-3-O-Geranylgeranylglyceryl Phosphate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4916
Polymers52,9102
Non-polymers5804
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-62 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.880, 95.880, 166.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein (S)-3-O-Geranylgeranylglyceryl Phosphate Synthase / E.C.2.5.1.42 / GGGPS / Protein pcrB homolog


Mass: 26455.082 Da / Num. of mol.: 2 / Fragment: GGGPS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea)
Description: three amino acids remain after removal of the his-tag, GSH
Gene: pcrB / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O29844, geranylgeranylglycerol-phosphate geranylgeranyltransferase
#2: Chemical ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9O6P
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, magnesium chloride, sodium citrate, sn-glycerol-1-phosphate (added during cryoprotection), 2-methyl-2,4-pentanediol (added during cryoprotection), pH 6.0, VAPOR DIFFUSION, HANGING ...Details: PEG 4000, magnesium chloride, sodium citrate, sn-glycerol-1-phosphate (added during cryoprotection), 2-methyl-2,4-pentanediol (added during cryoprotection), pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 31, 2004
RadiationMonochromator: Si (111) double-crystal monochromator, bent-flat Si-mirror (Rh coated)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNumber: 37366 / Rmerge(I) obs: 0.042 / Χ2: 1.656 / D res high: 2 Å / D res low: 100 Å / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.3110099.710.0271.716
3.424.3199.910.0281.816
2.993.4210010.0371.657
2.712.9910010.0461.601
2.522.7110010.0631.708
2.372.5210010.0841.665
2.252.3710010.1141.633
2.152.2510010.1471.582
2.072.1510010.1921.568
22.0710010.2581.604
ReflectionResolution: 2→50 Å / Num. all: 37366 / Num. obs: 37366 / % possible obs: 99.9 % / Rmerge(I) obs: 0.042 / Χ2: 1.656
Reflection shellResolution: 2→2.07 Å / % possible obs: 100 % / Rmerge(I) obs: 0.258 / Num. measured obs: 3746 / Χ2: 1.604 / % possible all: 100

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.779 / Packing: 0.521
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation4 Å15 Åfast direct99.9 0
Translation4 Å15 Ågeneral99.9 0

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Determined from a SeMet MAD experiment

Resolution: 2→50 Å / σ(F): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 1868 4.9 %random
Rwork0.1879 ---
all-37366 --
obs-35498 --
Solvent computationBsol: 49.654 Å2
Displacement parametersBiso mean: 34.415 Å2
Baniso -1Baniso -2Baniso -3
1--0.895 Å2-2.374 Å20 Å2
2---0.895 Å20 Å2
3---1.79 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 20 238 4025
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_mcbond_it4.0123.218
X-RAY DIFFRACTIONc_mcangle_it4.9684.262
X-RAY DIFFRACTIONc_scbond_it6.4815.018
X-RAY DIFFRACTIONc_scangle_it8.1326.605
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3g1p.par
X-RAY DIFFRACTION4mpd.par

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