[English] 日本語
Yorodumi- PDB-8cy8: apo form Cryo-EM structure of Campylobacter jejune ketol-acid red... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cy8 | ||||||
---|---|---|---|---|---|---|---|
Title | apo form Cryo-EM structure of Campylobacter jejune ketol-acid reductoisommerase crosslinked by Glutaraldehyde | ||||||
Components | Ketol-acid reductoisomerase (NADP(+)) | ||||||
Keywords | ISOMERASE / ketol-acid reductoisomerase / 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 | ELECTRON MICROSCOPY / single particle reconstruction / Resolution: 2.94 Å | ||||||
Authors | Zheng, S. / Guddat, L.W. | ||||||
Funding support | Australia, 1items
| ||||||
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, R.P. / Williams, S. / Kobe, B. / Schembri, M.A. / Landsberg, M.J. / Wu, B. / Bruck, T.B. / ...Authors: Lv, Y. / Zheng, S. / Goldenzweig, A. / Liu, F. / Gao, Y. / Yang, X. / Kandale, A. / McGeary, R.P. / Williams, S. / Kobe, B. / Schembri, M.A. / Landsberg, M.J. / Wu, B. / Bruck, T.B. / Sieber, V. / Boden, M. / Rao, Z. / Fleishman, S.J. / Schenk, G. / Guddat, L.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8cy8.cif.gz | 608.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8cy8.ent.gz | 515.4 KB | Display | PDB format |
PDBx/mmJSON format | 8cy8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cy8_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8cy8_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8cy8_validation.xml.gz | 98.7 KB | Display | |
Data in CIF | 8cy8_validation.cif.gz | 148.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/8cy8 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/8cy8 | HTTPS FTP |
-Related structure data
Related structure data | 27070MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 35665.953 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: ilvC, CW563_00670 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5T0UG45 #2: Chemical | ChemComp-PTD / Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Campylobacter jejuni ketol-acid reductoisomerase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 450 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Campylobacter jejuni (Campylobacter) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74899 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|