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Yorodumi- EMDB-27070: apo form Cryo-EM structure of Campylobacter jejune ketol-acid red... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27070 | |||||||||
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Title | apo form Cryo-EM structure of Campylobacter jejune ketol-acid reductoisommerase crosslinked by Glutaraldehyde | |||||||||
Map data | Campylobacter jejune ketol-acid reductoisommerase crosslinked by Glutaraldehyde | |||||||||
Sample |
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Keywords | ketol-acid reductoisomerase / Isomerase / enzyme stability / dodecamer / branched-chain amino acid | |||||||||
Function / homology | Function and homology information ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / isomerase activity / NADP binding / magnesium ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Campylobacter jejuni (Campylobacter) | |||||||||
Method | single particle reconstruction / Resolution: 2.94 Å | |||||||||
Authors | Zheng S / Guddat LW | |||||||||
Funding support | Australia, 1 items
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Citation | Journal: Appl Biosci / Year: 2022 Title: Enhancing the Thermal and Kinetic Stability of Ketol-Acid Reductoisomerase, a Central Catalyst of a Cell-Free Enzyme Cascade for the Manufacture of Platform Chemicals Authors: Lv Y / Zheng S / Goldenzweig A / Liu F / Gao Y / Yang X / Kandale A / McGeary RP / Williams S / Kobe B / Schembri MA / Landsberg MJ / Wu B / Bruck TB / Sieber V / Boden M / Rao Z / Fleishman ...Authors: Lv Y / Zheng S / Goldenzweig A / Liu F / Gao Y / Yang X / Kandale A / McGeary RP / Williams S / Kobe B / Schembri MA / Landsberg MJ / Wu B / Bruck TB / Sieber V / Boden M / Rao Z / Fleishman SJ / Schenk G / Guddat LW | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27070.map.gz | 323.6 MB | EMDB map data format | |
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Header (meta data) | emd-27070-v30.xml emd-27070.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_27070.png | 107.9 KB | ||
Filedesc metadata | emd-27070.cif.gz | 5.4 KB | ||
Others | emd_27070_half_map_1.map.gz emd_27070_half_map_2.map.gz | 318.4 MB 318.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27070 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27070 | HTTPS FTP |
-Validation report
Summary document | emd_27070_validation.pdf.gz | 973.7 KB | Display | EMDB validaton report |
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Full document | emd_27070_full_validation.pdf.gz | 973.2 KB | Display | |
Data in XML | emd_27070_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | emd_27070_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27070 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27070 | HTTPS FTP |
-Related structure data
Related structure data | 8cy8MC 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_27070.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Campylobacter jejune ketol-acid reductoisommerase crosslinked by Glutaraldehyde | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map 1
File | emd_27070_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_27070_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Campylobacter jejuni ketol-acid reductoisomerase
Entire | Name: Campylobacter jejuni ketol-acid reductoisomerase |
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Components |
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-Supramolecule #1: Campylobacter jejuni ketol-acid reductoisomerase
Supramolecule | Name: Campylobacter jejuni ketol-acid reductoisomerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Campylobacter jejuni (Campylobacter) |
Molecular weight | Theoretical: 450 kDa/nm |
-Macromolecule #1: Ketol-acid reductoisomerase (NADP(+))
Macromolecule | Name: Ketol-acid reductoisomerase (NADP(+)) / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Campylobacter jejuni (Campylobacter) |
Molecular weight | Theoretical: 35.665953 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ITVYYDKDCD LNLIKSKKVA IIGFGSQGHA HAMNLRDNGV NVTIGLREGS VSAVKAKNAG FEVMSVSEAS KIADVIMILA PDEIQADIF NVEIKPNLSE GKAIAFAHGF NIHYGQIVVP KGVDVIMIAP KAPGHTVRNE FTLGGGTPCL IAIHQDESKN A KNLALSYA ...String: ITVYYDKDCD LNLIKSKKVA IIGFGSQGHA HAMNLRDNGV NVTIGLREGS VSAVKAKNAG FEVMSVSEAS KIADVIMILA PDEIQADIF NVEIKPNLSE GKAIAFAHGF NIHYGQIVVP KGVDVIMIAP KAPGHTVRNE FTLGGGTPCL IAIHQDESKN A KNLALSYA SAIGGGRTGI IETTFKAETE TDLFGEQAVL CGGLSALIQA GFETLVEAGY EPEMAYFECL HEMKLIVDLI YQ GGIADMR YSISNTAEYG DYITGPKIIT EETKKAMKGV LKDIQNGVFA KDFILERRAG FARMHAERKN MNDSLIEKTG RNL RAMMPW IS UniProtKB: Ketol-acid reductoisomerase (NADP(+)) |
-Macromolecule #2: PENTANEDIAL
Macromolecule | Name: PENTANEDIAL / type: ligand / ID: 2 / Number of copies: 12 / Formula: PTD |
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Molecular weight | Theoretical: 100.116 Da |
Chemical component information | ChemComp-PTD: |
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74899 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |