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- EMDB-70254: S. mutans Phosphodiesterase GdpP with 5' pApA -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-70254
TitleS. mutans Phosphodiesterase GdpP with 5' pApA
Map data
Sample
  • Complex: Streptococcus mutans phosphodiesterase GdpP.
    • Protein or peptide: Cyclic-di-AMP phosphodiesterase
    • RNA: 5' pApA
KeywordsCyclic di-AMP specific phosphodiesterase / HYDROLASE / 5' pApA / HYDROLASE-RNA complex
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsShataer S / Parashar VK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119504 United States
CitationJournal: To Be Published
Title: S.mutans Phosphodiesterase GdpP with 5' pApA
Authors: Shataer S / Parashar VK
History
DepositionApr 18, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70254.png

Downloads & links

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Map

FileDownload / File: emd_70254.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 330. Å		0.83 Å/pix.
x 400 pix.
= 330. Å		0.83 Å/pix.
x 400 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.49424434 - 0.8086776
Average (Standard dev.)-0.000054254775 (±0.014134617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_70254_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70254_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Streptococcus mutans phosphodiesterase GdpP.

EntireName: Streptococcus mutans phosphodiesterase GdpP.
Components
  • Complex: Streptococcus mutans phosphodiesterase GdpP.
    • Protein or peptide: Cyclic-di-AMP phosphodiesterase
    • RNA: 5' pApA

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Supramolecule #1: Streptococcus mutans phosphodiesterase GdpP.

SupramoleculeName: Streptococcus mutans phosphodiesterase GdpP. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: C-terminal region of S.mutans GdpP with GGDEF, DHH, and DHHA1 domains.
Source (natural)Organism: Streptococcus mutans (bacteria) / Strain: NCTC 10449
Molecular weightTheoretical: 265 KDa

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Macromolecule #1: Cyclic-di-AMP phosphodiesterase

MacromoleculeName: Cyclic-di-AMP phosphodiesterase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
Source (natural)Organism: Streptococcus mutans (bacteria) / Strain: NCTC 10449
Molecular weightTheoretical: 67.248594 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MKHHHHHHHG AAGGKLITML DQMPVGVIQF DPETDKIEWF NPFAELIFTK EDGEFDGEFI SSVIKNRKEG SVDQTMEVGE NKYSVDIDL DNGIFYFFNL SRESENQRQG LDLQPVIGII SIDNYDDTIE SLADADVSQI NGFIANFISE FAQSREIFYR R VNMDRFYF ...String:
MKHHHHHHHG AAGGKLITML DQMPVGVIQF DPETDKIEWF NPFAELIFTK EDGEFDGEFI SSVIKNRKEG SVDQTMEVGE NKYSVDIDL DNGIFYFFNL SRESENQRQG LDLQPVIGII SIDNYDDTIE SLADADVSQI NGFIANFISE FAQSREIFYR R VNMDRFYF FTDYSVLDQL IQDKFEVLEQ FRKEAQERHL PLTLSMGISY GNANHSQIGQ IALKNLNIAL VRGGDQAVIR EN DEHKKLL YFGGGTVSTI KRSRTRTRAM MTAISDKIKT VDSVFVVGHK NLDMDALGAS VGMQAFANNI IEHAAYAVYD EDS MSHDVA RAVNRLKEDG HTQLLTVKEA IEQVSDNSLL VMVDHSKLQL TLSRELYNKF TEVIVIDHHR RDDDFPENAI LTFI ESGAS SASELVTELL QFQNGKYHLN KIQASIVMAG IMLDTKSFST RVTSRTFDVA SYLRTLGSDN VEIQNISALD FDEYR LINE LILRGDRILP NVVVATGADD ISYSNVIASK AADTMLNMAG IEATFVITRN DERTVCISAR SRNKINVQRI MEEMGG GGH FNLAACQLKG TSVKEARKLL LEKIKEEFTG NEEA

UniProtKB: Cyclic-di-AMP phosphodiesterase

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Macromolecule #2: 5' pApA

MacromoleculeName: 5' pApA / type: rna / ID: 2 / Number of copies: 1
EC number: Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
Source (natural)Organism: Streptococcus mutans (bacteria)
Molecular weightTheoretical: 613.454 Da
SequenceString:
AA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.93 µm / Nominal defocus min: 0.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48712
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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