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Yorodumi- EMDB-18606: Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPD... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18606 | |||||||||
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Title | Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPDH) ATP+IMP-bound form, extended | |||||||||
Map data | LocScale filtered map | |||||||||
Sample |
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Keywords | Octamer / ATP+IMP complex / Purine metabolism / IMPDH / OXIDOREDUCTASE | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||
Authors | Bulvas O / Kouba T / Pichova I | |||||||||
Funding support | European Union, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18606.map.gz | 103.1 MB | EMDB map data format | |
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Header (meta data) | emd-18606-v30.xml emd-18606.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18606_fsc.xml | 13.5 KB | Display | FSC data file |
Images | emd_18606.png | 121 KB | ||
Masks | emd_18606_msk_1.map | 209.3 MB | Mask map | |
Filedesc metadata | emd-18606.cif.gz | 6.6 KB | ||
Others | emd_18606_additional_1.map.gz emd_18606_half_map_1.map.gz emd_18606_half_map_2.map.gz | 195.5 MB 165.4 MB 165.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18606 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18606 | HTTPS FTP |
-Related structure data
Related structure data | 8qqvMC 17988 18184 18600 18601 18602 18604 18607 18608 8pw3C 8q65C 8qqpC 8qqqC 8qqrC 8qqtC 8qqwC 8qqxC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_18606.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | LocScale filtered map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8336 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18606_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Octameric assembly of inosine monophosphate dehydrogenase in comp...
Entire | Name: Octameric assembly of inosine monophosphate dehydrogenase in complex with ATP+IMP |
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Components |
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-Supramolecule #1: Octameric assembly of inosine monophosphate dehydrogenase in comp...
Supramolecule | Name: Octameric assembly of inosine monophosphate dehydrogenase in complex with ATP+IMP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Molecular weight | Theoretical: 426.658 KDa |
-Macromolecule #1: Inosine-5'-monophosphate dehydrogenase
Macromolecule | Name: Inosine-5'-monophosphate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: IMP dehydrogenase |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: MC2 155 |
Molecular weight | Theoretical: 53.388988 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSIAESSVPI AVPVPTGGDD PTKVAMLGLT FDDVLLLPAA SDVVPATADT SSQLTKRIRL RVPLVSSAMD TVTESRMAIA MARAGGMGV LHRNLPVAEQ AGQVETVKRS EAGMVTDPVT CSPDNTLAEV DAMCARFRIS GLPVVDDTGE LVGIITNRDM R FEVDQSKP ...String: MSIAESSVPI AVPVPTGGDD PTKVAMLGLT FDDVLLLPAA SDVVPATADT SSQLTKRIRL RVPLVSSAMD TVTESRMAIA MARAGGMGV LHRNLPVAEQ AGQVETVKRS EAGMVTDPVT CSPDNTLAEV DAMCARFRIS GLPVVDDTGE LVGIITNRDM R FEVDQSKP VSEVMTKAPL ITAKEGVSAE AALGLLRRHK IEKLPIVDGH GKLTGLITVK DFVKTEQFPL STKDSDGRLL VG AAVGVGD DAWTRAMTLV DAGVDVLIVD TAHAHNRGVL DMVSRLKQAV GERVDVVGGN VATRAAAAAL VEAGADAVKV GVG PGSICT TRVVAGVGAP QITAILEAVA ACKPYGVPVI ADGGLQYSGD IAKALAAGAS TAMLGSLLAG TAESPGELIF VNGK QFKSY RGMGSLGAMQ GRGAAKSYSK DRYFQDDVLS EDKLVPEGIE GRVPFRGPLG TVIHQLTGGL RAAMGYTGSA TIEQL QQAQ FVQITAAGLK ESHPHDITMT VEAPNYYTR UniProtKB: Inosine-5'-monophosphate dehydrogenase |
-Macromolecule #2: INOSINIC ACID
Macromolecule | Name: INOSINIC ACID / type: ligand / ID: 2 / Number of copies: 8 / Formula: IMP |
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Molecular weight | Theoretical: 348.206 Da |
Chemical component information | ChemComp-I: |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 29 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
Details: 50 mM HEPES (pH 7.5), 200 mM KCl, 5 mM DTT, 4 mM MgCl2 Ligand: 2 mM ATP + 1 mM IMP | |||||||||||||||||||||
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 11232 / Average exposure time: 2.0 sec. / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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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. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 70.33 / Target criteria: CC coefficient |
Output model | PDB-8qqv: |