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- PDB-8q65: Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPD... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8q65 | ||||||
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Title | Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPDH) ATP-bound form | ||||||
![]() | Inosine-5'-monophosphate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Octamer / ATP-bound complex / Purine metabolism / IMPDH | ||||||
Function / homology | ![]() IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å | ||||||
![]() | Bulvas, O. / Kouba, T. / Pichova, I. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPDH) apo form Authors: Bulvas, O. / Kouba, T. / Pichova, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 657.9 KB | Display | ![]() |
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PDB format | ![]() | 431.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 18184 ![]() 17988 ![]() 18600 ![]() 18601 ![]() 18602 ![]() 18604 ![]() 18606 ![]() 18607 ![]() 18608 ![]() 8pw3C ![]() 8qqpC ![]() 8qqqC ![]() 8qqrC ![]() 8qqtC ![]() 8qqvC ![]() 8qqwC ![]() 8qqxC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 53388.988 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: MC2 155 / Gene: guaB, MSMEG_1602 / Plasmid: pRSFDuet-1 / Production host: ![]() ![]() #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-MG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Octameric assembly of inosine monophosphate dehydrogenase in complex with ATP Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.426658 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: 50 mM HEPES (pH 7.5), 200 mM KCl, 5 mM DTT,2 mM MgCl2 Ligand: 0.3 mM ATP | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2900 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 6484 |
Image scans | Movie frames/image: 40 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2754934 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 317151 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | B value: 38.33 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: CC coefficient Details: Initial fitting was done in UCSF ChimeraX. Model refinement was done by iterative cycles of manual fitting with Coot and ISOLDE and automated fitting with phenix.real_space_refine. | ||||||||||||||||||||||||
Atomic model building | Accession code: A0QSU3 / Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.82 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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