3UDO | pdb_00003udo

Crystal structure of putative isopropylamlate dehydrogenase from Campylobacter jejuni

• PDB DOI: https://doi.org/10.2210/pdb3UDO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Campylobacter jejuni
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-10-28 Released: 2011-11-09 
• Deposition Author(s): Tkaczuk, K.L., Chruszcz, M., Blus, B.J., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.217 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Crystal structure of putative isopropylamlate dehydrogenase from Campylobacter jejuni

Tkaczuk, K.L., Chruszcz, M., Blus, B.J., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.53 kDa 
• Atom Count: 2,853 
• Modeled Residue Count: 355 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-isopropylmalate dehydrogenase	A	361	Campylobacter jejuni	Mutation(s): 1  Gene Names: leuB, Cj1718c EC: 1.1.1.85
UniProt
Find proteins for Q9PLW0 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PLW0  Go to UniProtKB:  Q9PLW0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.217 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33UDO

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.794	α = 90
b = 74.794	β = 90
c = 163.787	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
DM	model building
MLPHARE	phasing
RESOLVE	model building
CCP4	model building
ARP/wARP	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-09 
Deposition Author(s): Tkaczuk, K.L., Chruszcz, M., Blus, B.J., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-11-09
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-06
  Changes: Data collection, Structure summary