8CY8 | pdb_00008cy8

apo form Cryo-EM structure of Campylobacter jejune ketol-acid reductoisommerase crosslinked by Glutaraldehyde

PDB DOI: https://doi.org/10.2210/pdb8CY8/pdb
EM Map EMD-27070: EMDB EMDataResource

Classification: ISOMERASE
Organism(s): Campylobacter jejuni
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-23 Released: 2023-02-01
Deposition Author(s): Zheng, S., Guddat, L.W.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.94 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8CY8

This is version 1.2 of the entry. See complete history.

Literature

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

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.

(2022) Appl Biosci (Basel)

DOI: https://doi.org/10.3390/applbiosci1020011

Macromolecule Content

Total Structure Weight: 429.19 kDa
Atom Count: 28,800
Modeled Residue Count: 3,744
Deposited Residue Count: 3,936
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketol-acid reductoisomerase (NADP(+))	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	328	Campylobacter jejuni	Mutation(s): 0 Gene Names: ilvC, CW563_00670 EC: 1.1.1.86
UniProt
Find proteins for Q9PHN5 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PHN5 Go to UniProtKB: Q9PHN5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9PHN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTD (Subject of Investigation/LOI) Query on PTD Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth F] SDF format, chain S [auth G] SDF format, chain T [auth H] SDF format, chain U [auth I] SDF format, chain V [auth J] SDF format, chain W [auth K] SDF format, chain X [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth G] MOL2 format, chain T [auth H] MOL2 format, chain U [auth I] MOL2 format, chain V [auth J] MOL2 format, chain W [auth K] MOL2 format, chain X [auth L] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth G] mmCIF format, chain T [auth H] mmCIF format, chain U [auth I] mmCIF format, chain V [auth J] mmCIF format, chain W [auth K] mmCIF format, chain X [auth L]	M [auth A] N [auth B] O [auth D] P [auth D] Q [auth E] M [auth A], N [auth B], O [auth D], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	PENTANEDIAL C₅ H₈ O₂ SXRSQZLOMIGNAQ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.94 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP210101802

Revision History (Full details and data files)

Version 1.0: 2023-02-01
Type: Initial release
Version 1.1: 2024-06-12
Changes: Data collection, Database references
Version 1.2: 2025-05-14
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.