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- PDB-8ry1: CryoEM structure of M. smegmatis GMP reductase in complex with GM... -

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Basic information

Entry
Database: PDB / ID: 8ry1
TitleCryoEM structure of M. smegmatis GMP reductase in complex with GMP at pH 6.6, compressed conformation.
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
GUANOSINE-5'-MONOPHOSPHATE / GMP reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.85 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)420,07124
Polymers414,2598
Non-polymers5,81216
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 G
d_2ens_1chain B
d_3ens_1chain C
d_4ens_1chain D
d_5ens_1chain A
d_6ens_1chain F
d_7ens_1chain E
d_8ens_1chain H

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11VALVALPROPROGG2 - 4742 - 474
d_125GP5GP5GP5GPGU501
d_135GP5GP5GP5GPGV502
d_21VALVALPROPROBB2 - 4742 - 474
d_225GP5GP5GP5GPBK501
d_235GP5GP5GP5GPBL502
d_31VALVALPROPROCC2 - 4742 - 474
d_325GP5GP5GP5GPCM501
d_335GP5GP5GP5GPCN502
d_41VALVALPROPRODD2 - 4742 - 474
d_425GP5GP5GP5GPDO501
d_435GP5GP5GP5GPDP502
d_51VALVALPROPROAA2 - 4742 - 474
d_525GP5GP5GP5GPAI501
d_535GP5GP5GP5GPAJ502
d_61VALVALPROPROFF2 - 4742 - 474
d_625GP5GP5GP5GPFS501
d_635GP5GP5GP5GPFT502
d_71VALVALPROPROEE2 - 4742 - 474
d_725GP5GP5GP5GPEQ501
d_735GP5GP5GP5GPER502
d_81VALVALPROPROHH2 - 4742 - 474
d_825GP5GP5GP5GPHW501
d_835GP5GP5GP5GPHX502

NCS oper:
IDCodeMatrixVector
1given(-0.721761159046, -0.692136593207, 0.00278668935965), (-0.69213827072, 0.721764780274, 0.000464931893295), (-0.00233313061006, -0.00159320457224, -0.999996009092)260.86520941, 104.81786163, 216.81139731
2given(0.690752339333, -0.723089571599, 0.00163620019603), (-0.723088711015, -0.690754177541, -0.0011756753993), (0.00198033074153, -0.000371017358346, -0.999997970316)111.411633144, 260.831157486, 216.207279771
3given(0.721759681282, 0.692138218243, -0.00276574080173), (0.692139856784, -0.721763257706, -0.000467414145691), (-0.00231972528501, -0.00157691875759, -0.999996066093)-44.7912850828, 111.257637912, 216.807731116
4given(-0.690783103882, 0.723060430552, -0.00152222244101), (0.723059788463, 0.6907846743, 0.00103733283188), (0.00180158225717, -0.000384085842824, -0.999998303388)104.659901938, -44.7474680488, 216.228338556
5given(0.00123189388168, -0.999998622367, 0.00111252041075), (0.999998710914, 0.00123074672618, -0.00103122872297), (0.00102985807146, 0.00111378934097, 0.999998849432)216.025488936, -0.316919128933, -0.26304390846
6given(-0.999999979931, -0.0001616157432, -0.000118395373611), (0.000161595036777, -0.999999971652, 0.000174880851764), (-0.000118423633753, 0.00017486171615, 0.9999999777)216.119293513, 216.036880091, -0.0119658482388
7given(-0.00173882816507, 0.999997488429, -0.00141407636935), (-0.999997889409, -0.00173727785264, 0.00109683310679), (0.00109437370845, 0.00141598058911, 0.999998398671)0.14390384449, 216.457164988, -0.311693497045

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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
#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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 with GMP at pH 6.6 / Type: COMPLEX / Entity ID: #1 / 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: 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 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).
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 700 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
7UCSF ChimeraX1.5model fitting
12RELION43D reconstruction
13PHENIX1.21rc1_4985model refinement
14Coot0.9.8.1model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12596 / 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: 175.73 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003128096
ELECTRON MICROSCOPYf_angle_d0.750938312
ELECTRON MICROSCOPYf_chiral_restr0.04444536
ELECTRON MICROSCOPYf_plane_restr0.00495096
ELECTRON MICROSCOPYf_dihedral_angle_d4.30344336
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2JAELECTRON MICROSCOPYNCS constraints2.61798584861E-10
ens_1d_3JAELECTRON MICROSCOPYNCS constraints8.54234100751E-13
ens_1d_4JAELECTRON MICROSCOPYNCS constraints2.07124864387E-13
ens_1d_5JAELECTRON MICROSCOPYNCS constraints2.23244305393E-13
ens_1d_6JAELECTRON MICROSCOPYNCS constraints5.04069180918E-13
ens_1d_7JAELECTRON MICROSCOPYNCS constraints9.93821847825E-11
ens_1d_8JAELECTRON MICROSCOPYNCS constraints3.18161581964E-13

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