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Yorodumi- PDB-8qqt: Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qqt | ||||||
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Title | Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPDH) ATP+ppGpp-bound form, compressed | ||||||
Components | Inosine-5'-monophosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Octamer / ATP+ppGpp complex / Purine metabolism / IMPDH | ||||||
Function / homology | Function and homology information IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å | ||||||
Authors | Bulvas, O. / Kouba, T. / Pichova, I. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qqt.cif.gz | 823 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qqt.ent.gz | 549 KB | Display | PDB format |
PDBx/mmJSON format | 8qqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qqt_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 8qqt_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 8qqt_validation.xml.gz | 102.6 KB | Display | |
Data in CIF | 8qqt_validation.cif.gz | 155.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/8qqt ftp://data.pdbj.org/pub/pdb/validation_reports/qq/8qqt | HTTPS FTP |
-Related structure data
Related structure data | 18604MC 8pw3C 8q65C 8qqpC 8qqqC 8qqrC 8qqvC 8qqwC 8qqxC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: MC2 155 / Gene: guaB, MSMEG_1602 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): LOBSTR- -RIL / References: UniProt: A0QSU3, IMP dehydrogenase #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-G4P / #4: 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 |
-Sample preparation
Component | Name: Octameric assembly of inosine monophosphate dehydrogenase in complex with ATP+ppGpp Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.426658 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) | ||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: LOBSTR-BL21(DE3)-RIL / Plasmid: pRSFDuet-1 | ||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: 50 mM HEPES (pH 7.5), 200 mM KCl, 5 mM DTT, 2.5 mM MgCl2 Ligand: 0.5 mM ATP + 2 mM GTP + 1 mM IMP | ||||||||||||||||||||||||||||||||||||||||
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 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 2 sec. / Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 37330 |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 15670460 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 428872 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | B value: 50.05 / 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: 50.22 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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