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- PDB-9n0l: S.mutans Phosphodiesterase GdpP in the Presence of HEME-Cyanide -

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Basic information

Entry
Database: PDB / ID: 9n0l
TitleS.mutans Phosphodiesterase GdpP in the Presence of HEME-Cyanide
ComponentsCyclic-di-AMP phosphodiesterase
KeywordsHYDROLASE / Cyclic di-AMP specific phosphodiesterase
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / nucleic acid binding / hydrolase activity / metal ion binding / plasma membrane
Similarity search - Function
Cyclic-di-AMP phosphodiesterase GdpP/PdeA / : / Cyclic-di-AMP phosphodiesterase GdpP-like, PAS domain / Cyclic-di-AMP phosphodiesterase GdpP-like, GGDEF domain / : / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain
Similarity search - Domain/homology
Cyclic-di-AMP phosphodiesterase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsShataer, S. / Parashar, V.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119504 United States
CitationJournal: To Be Published
Title: Cryo-EM strucutre of C-terminal GdpP in the presence of HEME.
Authors: Shataer, S. / Parashar, V.K.
History
DepositionJan 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic-di-AMP phosphodiesterase
C: Cyclic-di-AMP phosphodiesterase
D: Cyclic-di-AMP phosphodiesterase
B: Cyclic-di-AMP phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)268,9944
Polymers268,9944
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, C2 Symmetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Cyclic-di-AMP phosphodiesterase


Mass: 67248.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: SMU82_00365 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A829BUJ0, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
Has protein modificationN

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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: Streptococcus mutans phosphodiesterase GdpP. / Type: COMPLEX
Details: C-terminal region of S.mutans GdpP with GGDEF, DHH, and DHHA1 domains.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.265 MDa / Experimental value: YES
Source (natural)Organism: Streptococcus mutans (bacteria) / Strain: NCTC 10449
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 / Plasmid: pQLinkH
Buffer solutionpH: 8
SpecimenEmbedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1930 nm / Nominal defocus min: 0 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67232 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 220.61 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002215316
ELECTRON MICROSCOPYf_angle_d0.499720656
ELECTRON MICROSCOPYf_chiral_restr0.04052396
ELECTRON MICROSCOPYf_plane_restr0.0022692
ELECTRON MICROSCOPYf_dihedral_angle_d5.10812118

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