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- PDB-7txv: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q wit... -

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Basic information

Entry
Database: PDB / ID: 7txv
TitleCyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q with ATP and 16x(Asp-Arg)
Components
  • 16x(Asp-Arg)
  • Cyanophycin synthase
KeywordsLIGASE / Cyanophycin / CphA1 / ATP-grasp / enzyme
Function / homology
Function and homology information


cyanophycin synthase (L-aspartate-adding) / cyanophycin synthase (L-arginine-adding) / cyanophycin synthetase activity (L-aspartate-adding) / cyanophycin synthetase activity (L-arginine-adding) / biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Cyanophycin synthase-like, N-terminal / Cyanophycin synthase-like N-terminal domain / Cyanophycin synthetase / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain ...Cyanophycin synthase-like, N-terminal / Cyanophycin synthase-like N-terminal domain / Cyanophycin synthetase / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / ATP-grasp fold / ATP-grasp fold profile. / Protein-Tyrosine Phosphatase; Chain A / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Cyanophycin synthetase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6714 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSharon, I. / Grogg, M. / Hilvert, D. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)178084 Canada
CitationJournal: Nat Commun / Year: 2022
Title: A cryptic third active site in cyanophycin synthetase creates primers for polymerization
Authors: Sharon, I. / Pinus, S. / Grogg, M. / Moitessier, N. / Hilvert, D. / Schmeing, T.M.
History
DepositionFeb 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyanophycin synthase
B: Cyanophycin synthase
C: Cyanophycin synthase
D: Cyanophycin synthase
E: 16x(Asp-Arg)
F: 16x(Asp-Arg)
G: 16x(Asp-Arg)
H: 16x(Asp-Arg)
I: 16x(Asp-Arg)
J: 16x(Asp-Arg)
K: 16x(Asp-Arg)
L: 16x(Asp-Arg)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)422,60640
Polymers417,89812
Non-polymers4,70828
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Cyanophycin synthase / Cyanophycin synthetase


Mass: 95757.852 Da / Num. of mol.: 4 / Mutation: E82Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6714 (bacteria) / Strain: PCC 6714 / Gene: cphA, D082_30240 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A068N621, cyanophycin synthase (L-aspartate-adding), cyanophycin synthase (L-arginine-adding)
#2: Protein/peptide
16x(Asp-Arg)


Mass: 4358.380 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationY

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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: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q with ATP and 16x(Asp-Arg)
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 383 kDa/nm / Experimental value: YES
Source (natural)Organism: Synechocystis sp. PCC 6714 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2-4158_final: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 318594 / Symmetry type: POINT
RefinementHighest resolution: 2.7 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.02228096
ELECTRON MICROSCOPYf_angle_d1.95938192
ELECTRON MICROSCOPYf_dihedral_angle_d12.73310564
ELECTRON MICROSCOPYf_chiral_restr0.1014384
ELECTRON MICROSCOPYf_plane_restr0.014992

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