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- PDB-6nke: Wild-type GGGPS from Thermoplasma volcanium -

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Basic information

Entry
Database: PDB / ID: 6nke
TitleWild-type GGGPS from Thermoplasma volcanium
ComponentsGeranylgeranylglyceryl phosphate synthase
KeywordsTRANSFERASE / Archaea Complex Tim-barrel Transferase
Function / homology
Function and homology information


: / phosphoglycerol geranylgeranyltransferase / phosphoglycerol geranylgeranyltransferase activity / glycerophospholipid biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
Geranylgeranylglyceryl phosphate synthase / 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
IMIDAZOLE / Geranylgeranylglyceryl phosphate synthase
Similarity search - Component
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsBlank, P.N. / Alderfer, K.E. / Gillott, B.N. / Christianson, D.W. / Himmelberger, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM56838 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structural studies of geranylgeranylglyceryl phosphate synthase, a prenyltransferase found in thermophilic Euryarchaeota.
Authors: Blank, P.N. / Barnett, A.A. / Ronnebaum, T.A. / Alderfer, K.E. / Gillott, B.N. / Christianson, D.W. / Himmelberger, J.A.
History
DepositionJan 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geranylgeranylglyceryl phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9246
Polymers27,5061
Non-polymers4185
Water3,891216
1
A: Geranylgeranylglyceryl phosphate synthase
hetero molecules

A: Geranylgeranylglyceryl phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,84912
Polymers55,0122
Non-polymers83710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4830 Å2
ΔGint-52 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.761, 73.761, 122.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-422-

HOH

21A-583-

HOH

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Components

#1: Protein Geranylgeranylglyceryl phosphate synthase / GGGPS / (S)-3-O-geranylgeranylglyceryl phosphate synthase / Phosphoglycerol geranylgeranyltransferase


Mass: 27506.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1) (archaea)
Strain: ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1
Gene: TV0745, TVG0750626 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q97AR4, phosphoglycerol geranylgeranyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8.04 / Details: 2.2M Ammonium Sulfate, 0.1M Tris pH 8.04 / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 298 K
Ambient temp details: Collected normally at room temperature while crystals were in cryostream
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.72→73.76 Å / Num. obs: 36732 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.023 / Rrim(I) all: 0.075 / Net I/σ(I): 15.2
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1916 / CC1/2: 0.791 / Rpim(I) all: 0.443 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JEJ

4jej


Resolution: 1.72→36.88 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.98
RfactorNum. reflection% reflection
Rfree0.2041 1873 5.11 %
Rwork0.1966 --
obs0.197 36624 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.72→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1867 0 27 218 2112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031975
X-RAY DIFFRACTIONf_angle_d0.6372672
X-RAY DIFFRACTIONf_dihedral_angle_d6.032074
X-RAY DIFFRACTIONf_chiral_restr0.05314
X-RAY DIFFRACTIONf_plane_restr0.005339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.76660.36981420.30812633X-RAY DIFFRACTION100
1.7666-1.81850.30941460.29012580X-RAY DIFFRACTION100
1.8185-1.87720.32771440.28762637X-RAY DIFFRACTION100
1.8772-1.94430.29981360.27962652X-RAY DIFFRACTION100
1.9443-2.02220.26341400.25022617X-RAY DIFFRACTION100
2.0222-2.11420.27531350.24752667X-RAY DIFFRACTION100
2.1142-2.22560.26961580.23632624X-RAY DIFFRACTION100
2.2256-2.36510.27321160.23762684X-RAY DIFFRACTION100
2.3651-2.54760.26051400.23672668X-RAY DIFFRACTION100
2.5476-2.80390.25211520.21992669X-RAY DIFFRACTION100
2.8039-3.20940.22371370.19742715X-RAY DIFFRACTION100
3.2094-4.04280.16551530.16192733X-RAY DIFFRACTION100
4.0428-36.88880.13931740.15352872X-RAY DIFFRACTION100

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