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- PDB-8a8e: PPSA C terminal octahedral structure -

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Basic information

Entry
Database: PDB / ID: 8a8e
TitlePPSA C terminal octahedral structure
ComponentsPhosphoenolpyruvate synthase
KeywordsBIOSYNTHETIC PROTEIN / enzyme / phosphorylation of pyruvate
Function / homology
Function and homology information


pyruvate, water dikinase / pyruvate, water dikinase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / metal ion binding
Similarity search - Function
Phosphoenolpyruvate synthase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / PEP-utilising enzyme, mobile domain ...Phosphoenolpyruvate synthase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / ATP-grasp fold, subdomain 1
Similarity search - Domain/homology
Phosphoenolpyruvate synthase
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSong, W.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: To Be Published
Title: Survival strategies in the heat Lysine acetylation stabilizes the quaternary structure of a Mega-Dalton hyperthermophilic PEP-synthase
Authors: Song, W.
History
DepositionJun 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate synthase
B: Phosphoenolpyruvate synthase
C: Phosphoenolpyruvate synthase
D: Phosphoenolpyruvate synthase
E: Phosphoenolpyruvate synthase
F: Phosphoenolpyruvate synthase
G: Phosphoenolpyruvate synthase
H: Phosphoenolpyruvate synthase
I: Phosphoenolpyruvate synthase
J: Phosphoenolpyruvate synthase
K: Phosphoenolpyruvate synthase
L: Phosphoenolpyruvate synthase
M: Phosphoenolpyruvate synthase
N: Phosphoenolpyruvate synthase
O: Phosphoenolpyruvate synthase
P: Phosphoenolpyruvate synthase
Q: Phosphoenolpyruvate synthase
R: Phosphoenolpyruvate synthase
S: Phosphoenolpyruvate synthase
T: Phosphoenolpyruvate synthase
U: Phosphoenolpyruvate synthase
V: Phosphoenolpyruvate synthase
W: Phosphoenolpyruvate synthase
X: Phosphoenolpyruvate synthase


Theoretical massNumber of molelcules
Total (without water)2,174,42224
Polymers2,174,42224
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Phosphoenolpyruvate synthase / PEP synthase / Pyruvate / water dikinase


Mass: 90600.922 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: ppsA, PF0043 / Production host: Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: P42850, pyruvate, water dikinase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Phosphoenolpyruvate synthase / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 2.3 MDa / Experimental value: YES
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium ChlorideNaCl1
22 mMMagnesium chlorideMgCl21
325 mMHEPES sodium saltHEPES1
SpecimenConc.: 2 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingDetails: The sample was plunged freeze in ethane-propane and transfer to liquid nitrogen.
Material: Ice
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 298.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 1 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142247 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
RefinementCross valid method: NONE

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