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- PDB-5jfq: Geranylgeranyl Pyrophosphate Synthetase from archaeon Geoglobus a... -

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Basic information

Entry
Database: PDB / ID: 5jfq
TitleGeranylgeranyl Pyrophosphate Synthetase from archaeon Geoglobus acetivorans
ComponentsGeranylgeranyl Pyrophosphate Synthetase
KeywordsOXIDOREDUCTASE / Geranylgeranyl Pyrophosphate Synthetase / hyperthermophilic / archaeon
Function / homology
Function and homology information


geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / metal ion binding
Similarity search - Function
Polyprenyl synthases signature 1. / 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
Geranylgeranyl pyrophosphate synthase
Similarity search - Component
Biological speciesGeoglobus acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsPetrova, T. / Boyko, K.M. / Nikolaeva, A.Y. / Stekhanova, T.N. / Mardanov, A.V. / Rakitin, A.L. / Ravin, N.V. / Popov, V.O.
CitationJournal: Extremophiles / Year: 2018
Title: Structural characterization of geranylgeranyl pyrophosphate synthase GACE1337 from the hyperthermophilic archaeon Geoglobus acetivorans.
Authors: Petrova, T.E. / Boyko, K.M. / Nikolaeva, A.Y. / Stekhanova, T.N. / Gruzdev, E.V. / Mardanov, A.V. / Stroilov, V.S. / Littlechild, J.A. / Popov, V.O. / Bezsudnova, E.Y.
History
DepositionApr 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2Jan 10, 2024Group: 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: Geranylgeranyl Pyrophosphate Synthetase
B: Geranylgeranyl Pyrophosphate Synthetase


Theoretical massNumber of molelcules
Total (without water)72,5012
Polymers72,5012
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-36 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.860, 85.860, 188.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Geranylgeranyl Pyrophosphate Synthetase


Mass: 36250.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Protein: AIY90378 / Source: (gene. exp.) Geoglobus acetivorans (archaea) / Gene: GACE_1337 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): DLT1270 / References: UniProt: A0A0A7GEY4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Tris pH 8.0, 0.1M sodium malonate pH 8.0, 33% PEG 1000 and 10% ethylene glycol mixed with protein in ratio 1:1 over 500 ml of precipitant solution covered with oils

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→94.08 Å / Num. obs: 24891 / % possible obs: 99.8 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.309 / Net I/σ(I): 6.7
Reflection shellResolution: 2.51→2.62 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2405: ???)refinement
MOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WY0

1wy0


Resolution: 2.51→78.112 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.27 / Phase error: 29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 2297 5.04 %
Rwork0.2048 --
obs0.2077 24725 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→78.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 0 0 36 4668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094701
X-RAY DIFFRACTIONf_angle_d1.0096355
X-RAY DIFFRACTIONf_dihedral_angle_d14.3432833
X-RAY DIFFRACTIONf_chiral_restr0.05739
X-RAY DIFFRACTIONf_plane_restr0.005820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5101-2.56470.34661380.30632632X-RAY DIFFRACTION97
2.5647-2.62440.36591490.30522694X-RAY DIFFRACTION98
2.6244-2.690.39921670.2772668X-RAY DIFFRACTION98
2.69-2.76270.3171290.2672687X-RAY DIFFRACTION98
2.7627-2.8440.33611140.25842707X-RAY DIFFRACTION99
2.844-2.93580.32461450.24922672X-RAY DIFFRACTION100
2.9358-3.04080.3181450.25282796X-RAY DIFFRACTION100
3.0408-3.16250.31951410.23422694X-RAY DIFFRACTION100
3.1625-3.30640.30871420.23272732X-RAY DIFFRACTION100
3.3064-3.48080.26351370.21392725X-RAY DIFFRACTION100
3.4808-3.69880.25451560.19832703X-RAY DIFFRACTION100
3.6988-3.98440.27111860.19072676X-RAY DIFFRACTION100
3.9844-4.38540.19781340.1612728X-RAY DIFFRACTION100
4.3854-5.01980.19631350.16722741X-RAY DIFFRACTION100
5.0198-6.3240.30141220.20472720X-RAY DIFFRACTION99
6.324-78.14980.18311570.16852711X-RAY DIFFRACTION99

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