3KN3 | pdb_00003kn3

Crystal Structure of LysR Substrate Binding Domain (25-263) of Putative Periplasmic Protein from Wolinella succinogenes

• PDB DOI: https://doi.org/10.2210/pdb3KN3/pdb

• Classification: TRANSCRIPTION
• Organism(s): Wolinella succinogenes
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-11-11 Released: 2009-12-01 
• Deposition Author(s): Kim, Y., Volkart, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.229 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Crystal Structure of LysR Substrate Binding Domain from Wolinella succinogenes

Kim, Y., Volkart, L., Bearden, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 82.93 kDa 
• Atom Count: 5,944 
• Modeled Residue Count: 712 
• Deposited Residue Count: 726 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE PERIPLASMIC PROTEIN	A, B, C	242	Wolinella succinogenes	Mutation(s): 0  Gene Names: WS1370
UniProt
Find proteins for Q7M8V9 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W)) Explore Q7M8V9  Go to UniProtKB:  Q7M8V9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	I [auth B]	Glutathione C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
CIT	J [auth C]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	D [auth A], E [auth A], G [auth A], H [auth B], K [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	F [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

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

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH)	I [auth B]	Glutathione	Peptide-like / Oxidation-reduction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.229 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.784	α = 90
b = 81.29	β = 103.32
c = 87.91	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-01 
Deposition Author(s): Kim, Y., Volkart, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2011-12-21
  Changes: Non-polymer description
• Version 1.3: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary