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- PDB-2f6u: Crystal Structure of (S)-3-O-Geranylgeranylglyceryl Phosphate Syn... -

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Basic information

Entry
Database: PDB / ID: 2f6u
TitleCrystal Structure of (S)-3-O-Geranylgeranylglyceryl Phosphate Synthase complexed with citrate
Components(S)-3-O-Geranylgeranylglyceryl Phosphate Synthase
KeywordsTRANSFERASE / non-canonical TIM-barrel / prenyltransferase / archaeal lipid synthesis / dimer
Function / homology
Function and homology information


phosphoglycerol geranylgeranyltransferase / phosphoglycerol geranylgeranyltransferase activity / glycerophospholipid biosynthetic process / polyprenyltransferase activity / 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
CITRIC ACID / Geranylgeranylglyceryl phosphate synthase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPayandeh, J.
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 1.3Feb 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)53,2944
Polymers52,9102
Non-polymers3842
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-21 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.240, 95.240, 166.620
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, magnesium chloride, sodium citrate, 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: 76814 / Rmerge(I) obs: 0.051 / Χ2: 1.509 / D res high: 1.55 Å / D res low: 100 Å / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
3.3410099.910.0371.743
2.653.3410010.0421.969
2.322.6510010.051.724
2.12.3210010.0591.606
1.952.110010.0711.567
1.841.9510010.0941.46
1.751.8410010.1261.282
1.671.7510010.1781.198
1.611.6710010.2321.193
1.551.6110010.2941.176
ReflectionResolution: 1.55→50 Å / Num. all: 76814 / Num. obs: 76814 / % possible obs: 99.9 % / Rmerge(I) obs: 0.051 / Χ2: 1.509
Reflection shellResolution: 1.55→1.61 Å / % possible obs: 100 % / Rmerge(I) obs: 0.294 / Num. measured obs: 7690 / Χ2: 1.176 / % possible all: 100

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.817 / Packing: 0.529
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation4 Å15 Åfast direct100 0
Translation4 Å15 Ågeneral100 0

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
CNSrefinement
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Determined from a SeMet MAD experiment

Resolution: 1.55→50 Å / σ(F): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 3841 4.9 %random
Rwork0.1911 ---
all-76814 --
obs-72973 --
Solvent computationBsol: 43.024 Å2
Displacement parametersBiso mean: 21.401 Å2
Baniso -1Baniso -2Baniso -3
1-0.602 Å2-0.346 Å20 Å2
2--0.602 Å20 Å2
3----1.204 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 0 26 340 4146
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_mcbond_it1.8651.25
X-RAY DIFFRACTIONc_mcangle_it2.6662
X-RAY DIFFRACTIONc_scbond_it3.6662.15
X-RAY DIFFRACTIONc_scangle_it5.3652.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3cit.par

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