5KSW

DHODB-I74D mutant

• PDB DOI: https://doi.org/10.2210/pdb5KSW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lactococcus lactis, Lactococcus lactis subsp. lactis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-07-10 Released: 2016-08-03 
• Deposition Author(s): Pompeu, Y.A., Stewart, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 0.244 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Literature

Isoleucine 74 Plays a Key Role in Controlling Electron Transfer Between Lactococcus lactis Dihydroorotate Dehydrogenase 1B Subunits

Pompeu, Y.A., Stewart, J.D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 125.44 kDa 
• Atom Count: 9,054 
• Modelled Residue Count: 1,135 
• Deposited Residue Count: 1,136 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase	A, D [auth C]	306	Lactococcus lactis	Mutation(s): 1  Gene Names: pyrD, LG36_1039 EC: 1.3.1.14
UniProt
Find proteins for Q9CFW8 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CFW8  Go to UniProtKB:  Q9CFW8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit	B, C [auth D]	262	Lactococcus lactis subsp. lactis	Mutation(s): 0  Gene Names: pyrK, NCDO895_2366
UniProt
Find proteins for Q9CFW7 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CFW7  Go to UniProtKB:  Q9CFW7

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	H [auth B], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
FMN	E [auth A], M [auth C]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
FES	I [auth B], L [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
EDO	G [auth A], N [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	F [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 0.244 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.99	α = 90
b = 151.72	β = 90
c = 214.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-03 
Deposition Author(s): Pompeu, Y.A., Stewart, J.D.

Revision History  

• Version 1.0: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2016-08-10
  Changes: Data collection
• Version 1.2: 2017-04-26
  Changes: Structure summary
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence
• Version 1.4: 2017-11-01
  Changes: Author supporting evidence
• Version 1.5: 2023-10-04
  Changes: Data collection, Database references, Refinement description