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- PDB-8ry7: CryoEM structure of M. smegmatis GMP reductase apoform at pH 6.6,... -

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Basic information

Entry
Database: PDB / ID: 8ry7
TitleCryoEM structure of M. smegmatis GMP reductase apoform at pH 6.6, extended conformation II.
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: 3.7 Å
AuthorsDolezal, M. / Kouba, T. / 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: Additional map / Part number: 1 / Data content type: Additional map / 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
E: GMP reductase
F: GMP reductase
G: GMP reductase
H: GMP reductase


Theoretical massNumber of molelcules
Total (without water)414,2598
Polymers414,2598
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 A
d_4ens_1chain D
d_5ens_1chain E
d_6ens_1chain F
d_7ens_1chain G
d_8ens_1chain H

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_3AA
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH

NCS oper:
IDCodeMatrixVector
1given(-0.00279829314261, -0.999976174998, 0.00631022911505), (0.999953892042, -0.00285608583915, -0.00916823665456), (0.00918604077733, 0.00628428274951, 0.999938060304)366.708069614, 2.15941485589, -2.72608592596
2given(-0.999999999148, 4.16859493696E-6, -4.10637767821E-5), (-4.17028260947E-6, -0.999999999147, 4.10988138923E-5), (-4.10636054228E-5, 4.10989851048E-5, 0.999999998312)366.785651362, 366.78170219, -0.00776157138432
3given(0.00233982410174, 0.999977261728, -0.0063246541991), (-0.999954030584, 0.00239848621419, 0.00928353290435), (0.00929849140876, 0.0063026416244, 0.999936905393)0.148326631377, 364.691289028, -2.74764297895
4given(0.258980529278, -0.965875145396, -0.00378007415271), (-0.965517411553, -0.258988244734, 0.026480503725), (-0.0265558551553, -0.00320820745884, -0.999642182964)314.112023586, 403.829094046, 371.259567595
5given(0.963471249776, 0.267733690307, 0.00646698768112), (0.267699050799, -0.963485433177, 0.00574789160528), (0.00776975265826, -0.00380672184475, -0.999962569206)-43.4282983944, 310.162183141, 365.722211609
6given(-0.258467484377, 0.96601231217, 0.0038434691787), (0.965656497733, 0.258477322942, -0.0264007937531), (-0.0264969414407, -0.00311227576068, -0.999644049567)52.5563547587, -36.9692350593, 371.234174487
7given(-0.963309357909, -0.268315504467, -0.00647078256685), (-0.268281750462, 0.963324021963, -0.00563303458), (0.00774489080256, -0.00369036205044, -0.99996319827)410.313016926, 56.7151199795, 365.699791296

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Components

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


Mass: 51782.434 Da / Num. of mol.: 8
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 6.6 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pTriex
Buffer solutionpH: 6.6
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 6.6, 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: 3000 nm / Nominal defocus min: 900 nm / C2 aperture diameter: 30 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
7UCSF ChimeraX1.5model fitting
10RELION4final Euler assignment
13Coot0.9.8.1model refinement
14PHENIX1.21rc1_4985model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18832 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Details: The 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 ...Details: The 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.
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 146.14 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003827752
ELECTRON MICROSCOPYf_angle_d0.640837776
ELECTRON MICROSCOPYf_chiral_restr0.04374496
ELECTRON MICROSCOPYf_plane_restr0.00385000
ELECTRON MICROSCOPYf_dihedral_angle_d3.28284064
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints8.9084676809E-13
ens_1d_3CCELECTRON MICROSCOPYNCS constraints3.83942392055E-11
ens_1d_4CCELECTRON MICROSCOPYNCS constraints5.03821452101E-13
ens_1d_5CCELECTRON MICROSCOPYNCS constraints9.1635894532E-13
ens_1d_6CCELECTRON MICROSCOPYNCS constraints9.54691861776E-11
ens_1d_7CCELECTRON MICROSCOPYNCS constraints1.16338323548E-10
ens_1d_8CCELECTRON MICROSCOPYNCS constraints1.08295796464E-12

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