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- EMDB-19584: CryoEM structure of M. smegmatis GMP reductase in complex with GM... -

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Basic information

Entry
Database: EMDB / ID: EMD-19584
TitleCryoEM structure of M. smegmatis GMP reductase in complex with GMP at pH 6.6, compressed conformation.
Map dataLAFTER de-noised
Sample
  • Complex: Msm GMPR with GMP at pH 6.6
    • Protein or peptide: GMP reductase
  • Ligand: GUANOSINE-5'-MONOPHOSPHATE
KeywordsGMP reductase / GuaB1 / CBS domain / Mycobacterium smegmatis / OXIDOREDUCTASE
Function / homology
Function and homology information


GMP reductase / GMP reductase activity / IMP salvage / IMP dehydrogenase activity / purine ribonucleoside salvage / cytosol
Similarity search - Function
GMP reductase-like / : / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
Biological speciesMycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsDolezal M / Kouba T / Pichova I
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Union (EU)LX22NPO5103European Union
CitationJournal: To Be Published
Title: Structural basis for allosteric regulation of mycobacterial guanosine 5'-monophosphate reductase with ATP and GTP.
Authors: Dolezal M / Knejzlik Z / Kouba T / Filimonenko A / Svachova H / Klima M / Pichova I
History
DepositionFeb 8, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19584.png

Downloads & links

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Map

FileDownload / File: emd_19584.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLAFTER de-noised
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.77 Å/pix.
x 280 pix.
= 216.076 Å		0.77 Å/pix.
x 280 pix.
= 216.076 Å		0.77 Å/pix.
x 280 pix.
= 216.076 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7717 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.36207035 - 0.5327768
Average (Standard dev.)0.0030091605 (±0.022750923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 216.076 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19584_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: RELION refined

Fileemd_19584_additional_1.map
AnnotationRELION refined
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19584_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_19584_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Msm GMPR with GMP at pH 6.6

EntireName: Msm GMPR with GMP at pH 6.6
Components
  • Complex: Msm GMPR with GMP at pH 6.6
    • Protein or peptide: GMP reductase
  • Ligand: GUANOSINE-5'-MONOPHOSPHATE

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Supramolecule #1: Msm GMPR with GMP at pH 6.6

SupramoleculeName: Msm GMPR with GMP at pH 6.6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155

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Macromolecule #1: GMP reductase

MacromoleculeName: GMP reductase / type: protein_or_peptide / ID: 1 / Details: Guanosine 5'-monophosphate reductase / Number of copies: 8 / Enantiomer: LEVO / EC number: GMP reductase
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 51.782434 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVRFLDGHTP AYDLTYNDVF VVPGRSDVAS RFDVDLSTVD GSGTTIPVVV ANMTAVAGRR MAETVARRGG IVVLPQDLPI TAVSETVDF VKSRDLVVDT PVTLSPEDSV SDANALLHKR AHGAAVVVFE GRPIGLVTEA NCAGVDRFAR VRDIALSDFV T APVGTDPR ...String:
MVRFLDGHTP AYDLTYNDVF VVPGRSDVAS RFDVDLSTVD GSGTTIPVVV ANMTAVAGRR MAETVARRGG IVVLPQDLPI TAVSETVDF VKSRDLVVDT PVTLSPEDSV SDANALLHKR AHGAAVVVFE GRPIGLVTEA NCAGVDRFAR VRDIALSDFV T APVGTDPR EVFDLLEHAP IDVAVMTAPD GTLAGVLTRT GAIRAGIYTP AVDAKGRLRI AAAVGINGDV GAKAQALAEA GA DLLVIDT AHGHQAKMLD AIKAVASLDL GLPLVAGNVV SAEGTRDLIE AGASIVKVGV GPGAMCTTRM MTGVGRPQFS AVV ECAAAA RQLGGHVWAD GGVRHPRDVA LALAAGASNV MIGSWFAGTY ESPGDLLFDR DDRPYKESYG MASKRAVAAR TAGD SSFDR ARKGLFEEGI STSRMSLDPA RGGVEDLLDH ITSGVRSTCT YVGAANLPEL HEKVVLGVQS AAGFAEGHPL PAGWT AAAK EDLEHHHHHH HH

UniProtKB: GMP reductase

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Macromolecule #2: GUANOSINE-5'-MONOPHOSPHATE

MacromoleculeName: GUANOSINE-5'-MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 16 / Formula: 5GP
Molecular weightTheoretical: 363.221 Da
Chemical component information

ChemComp-5GP:
GUANOSINE-5'-MONOPHOSPHATE

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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: 6.6
Component:
ConcentrationFormulaName
50.0 mMHEPES2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acid
100.0 mMKClPotassium chloride
2.0 mMMgCl2Magnesium chloride
VitrificationCryogen name: ETHANE
Details20 mg/ml Msm GMPR with 2 mM GMP in the storage buffer (50 mM Tris, pH 8.0, 2.5 mM TCEP) was diluted with the cryoEM buffer (50 mM HEPES, pH 6.6, 100 mM KCl, 2 mM MgCl2).

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7r50

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 12596
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsThe initial structure was obtained by rigid-body fitting an appropriate model into the cryo-EM map using ChimeraX. Phenix.real_space_refine with tight reference model restraints to the starting model was then used to remove the worst clashes.
RefinementSpace: REAL
Output model

PDB-8ry1:
CryoEM structure of M. smegmatis GMP reductase in complex with GMP at pH 6.6, compressed conformation.

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