4PZJ | pdb_00004pzj

1.60 Angstrom resolution crystal structure of a transcriptional regulator of the LysR family from Eggerthella lenta DSM 2243

• PDB DOI: https://doi.org/10.2210/pdb4PZJ/pdb

• Classification: TRANSCRIPTION
• Organism(s): Eggerthella lenta DSM 2243
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-03-31 Released: 2014-04-23 
• Deposition Author(s): Halavaty, A.S., Filippova, E.V., Minasov, G., Kiryukhina, O., Endres, M., Shuvalova, L., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.213 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.190 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

1.60 Angstrom resolution crystal structure of a transcriptional regulator of the LysR family from Eggerthella lenta DSM 2243

Halavaty, A.S., Filippova, E.V., Minasov, G., Kiryukhina, O., Endres, M., Shuvalova, L., Joachimiak, A., Anderson, W.F.

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: 8.21 kDa 
• Atom Count: 651 
• Modeled Residue Count: 70 
• Deposited Residue Count: 70 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, LysR family	A	70	Eggerthella lenta DSM 2243	Mutation(s): 0  Gene Names: Elen_0221
UniProt
Find proteins for C8WJY2 (Eggerthella lenta (strain ATCC 25559 / DSM 2243 / CCUG 17323 / JCM 9979 / KCTC 3265 / NCTC 11813 / VPI 0255 / 1899 B)) Explore C8WJY2  Go to UniProtKB:  C8WJY2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.213 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.190 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.623	α = 90
b = 31.623	β = 90
c = 132.34	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-23 
Deposition Author(s): Halavaty, A.S., Filippova, E.V., Minasov, G., Kiryukhina, O., Endres, M., Shuvalova, L., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-04-23
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary