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- EMDB-46862: Streptococcus pneumoniae GapN -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-46862
TitleStreptococcus pneumoniae GapN
Map data
Sample
  • Complex: apo GAPN
    • Protein or peptide: glyceraldehyde-3-phsphate dehydrogenase
Keywordsapo GAPN / OXIDOREDUCTASE
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / lactaldehyde dehydrogenase (NAD+) activity
Similarity search - Function
: / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsEunjeong L / Elan ZE
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Biochemical, structural, and biologial studies of Streptococcus pneumoniae GapN reveal a key metabolic player necessary for host infection.
Authors: Eunjeong L / Elan ZE
History
DepositionSep 3, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46862.png

Downloads & links

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Map

FileDownload / File: emd_46862.map.gz / Format: CCP4 / Size: 52.7 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 240 pix.
= 199.2 Å		0.83 Å/pix.
x 240 pix.
= 199.2 Å		0.83 Å/pix.
x 240 pix.
= 199.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.85064036 - 1.3125134
Average (Standard dev.)0.0013877827 (±0.054295823)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 199.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46862_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_46862_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 : apo GAPN

EntireName: apo GAPN
Components
  • Complex: apo GAPN
    • Protein or peptide: glyceraldehyde-3-phsphate dehydrogenase

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Supramolecule #1: apo GAPN

SupramoleculeName: apo GAPN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus pneumoniae (bacteria)

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Macromolecule #1: glyceraldehyde-3-phsphate dehydrogenase

MacromoleculeName: glyceraldehyde-3-phsphate dehydrogenase / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTRYQNLVNG KWKSSEQEIT IYSPINQEEL GTVPAMTQTE ADEAMQAARA ALPAWRALSA IERAAYLHKT AAILERDKEK IGTILAKEVA KGIKAAIGEV VRTADLIRYA AEEGLRITGQ AMEGGGFEAA SKNKLAVVRR EPVGIVLAIA PFNYPVNLSA SKIAPALIAG ...String:
MTRYQNLVNG KWKSSEQEIT IYSPINQEEL GTVPAMTQTE ADEAMQAARA ALPAWRALSA IERAAYLHKT AAILERDKEK IGTILAKEVA KGIKAAIGEV VRTADLIRYA AEEGLRITGQ AMEGGGFEAA SKNKLAVVRR EPVGIVLAIA PFNYPVNLSA SKIAPALIAG NVVMLKPPTQ GSISGLLLAK AFEEAGIPAG VFNTITGRGS EIGDYIIEHK EVNFINFTGS TPIGERIGRL AGMRPIMLEL GGKDAALVLE DADLEHAAKQ IVAGAFSYSG QRCTAIKRVI VLESVADKLA TLLQEEVSKL TVGDPFDNAD ITPVIDNASA DFIWGLIEDA QEKEAQALTP IKREGNLLWP VLFDQVTKDM KVAWEEPFGP VLPIIRVASV EEAIAFANES EFGLQSSVFT NDFKKAFEIA EKLEVGTVHI NNKTQRGPDN FPFLGVKGSG AGVQGIKYSI EAMTNVKSIV FDVK

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: OTHER / Number images used: 2301844
Initial angle assignmentType: OTHER
Final angle assignmentType: NOT APPLICABLE

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