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- PDB-8rya: CryoEM structure of M. smegmatis GMP reductase apoform at pH 7.8,... -

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Basic information

Entry
Database: PDB / ID: 8rya
TitleCryoEM structure of M. smegmatis GMP reductase apoform at pH 7.8, tetramer.
ComponentsGMP reductase
KeywordsOXIDOREDUCTASE / GMP reductase / GuaB1 / CBS domain / Mycobacterium smegmatis
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsDolezal, M. / Kouba, T. / Svachova, H. / Pichova, I.
Funding supportEuropean Union, 1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data 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: GMP reductase
B: GMP reductase
C: GMP reductase
D: GMP reductase


Theoretical massNumber of molelcules
Total (without water)207,1304
Polymers207,1304
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain C
d_2ens_1chain B
d_3ens_1chain D
d_4ens_1chain A

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 2 - 470 / Label seq-ID: 2 - 470

Dom-IDAuth asym-IDLabel asym-ID
d_1CC
d_2BB
d_3DD
d_4AA

NCS oper:
IDCodeMatrixVector
1given(-1.03698753695E-7, 1, -2.37340908065E-9), (-1, -1.03698753806E-7, -6.40351039996E-8), (-6.40351042457E-8, 2.37340244029E-9, 1)2.71040162829E-5, 470.151395394, 1.57531488583E-5
2given(-1.73328511544E-7, -1, 1.25599045049E-7), (1, -1.73328517317E-7, -4.56048192254E-8), (4.56048409953E-8, 1.25599037144E-7, 1)470.151391708, 5.6486376991E-5, -4.43241270887E-5
3given(-0.99999999339, 8.53725955603E-5, 7.70222512517E-5), (-8.54102626487E-5, -0.999999876708, -0.000489170972261), (7.69804799599E-5, -0.000489177547518, 0.99999987739)470.11216747, 470.301271062, 0.112105528129

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Components

#1: Protein
GMP reductase / Guanosine 5'-monophosphate reductase / GMPR


Mass: 51782.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Guanosine 5'-monophosphate reductase / Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: guaB1, MSMEG_3634, MSMEI_3548 / Plasmid: pTriex / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QYE8, GMP reductase
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: Msm GMPR apoform at pH 7.8 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pTriex
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acidHEPES1
2100 mMPotassium chlorideKCl1
32 mMMagnesium chlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 20 mg/ml Msm GMPR in the storage buffer (50 mM Tris, pH 8.0, 2.5 mM TCEP) was diluted with the cryoEM buffer (50 mM HEPES, pH 7.8, 100 mM KCl, 2 mM MgCl2).
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: 3300 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
7MOLREP11.9.02model fitting
8UCSF ChimeraX1.5model fitting
13RELION43D reconstruction
20PHENIX1.21rc1_4985model refinement
21Coot0.9.8.1model refinement
22ISOLDE1.5model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 258783 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Details: The initial structure was obtained by fitting an appropriate model into the cryo-EM map using MolRep and ChimeraX. The structure was then refined by iterative manual rebuilding in Coot and ...Details: The initial structure was obtained by fitting an appropriate model into the cryo-EM map using MolRep and ChimeraX. The structure was then refined by iterative manual rebuilding in Coot and Isolde, and automatic refinement in phenix.real_space_refine.
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 77.68 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002613856
ELECTRON MICROSCOPYf_angle_d0.529818876
ELECTRON MICROSCOPYf_chiral_restr0.04162252
ELECTRON MICROSCOPYf_plane_restr0.00492500
ELECTRON MICROSCOPYf_dihedral_angle_d4.65732036
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints1.07112825802E-12
ens_1d_3CCELECTRON MICROSCOPYNCS constraints1.73492006346E-12
ens_1d_4CCELECTRON MICROSCOPYNCS constraints1.0230773794E-11

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