4RYK | pdb_00004ryk

Crystal structure of a putative transcriptional regulator from Listeria monocytogenes EGD-e

• PDB DOI: https://doi.org/10.2210/pdb4RYK/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-15 Released: 2015-01-07 
• Deposition Author(s): Filippova, E.V., Wawrzak, Z., Minasov, G., Kiryukhina, O., Jedrzejczak, R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.199 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Crystal structure of a putative transcriptional regulator from Listeria monocytogenes EGD-e

Filippova, E.V., Wawrzak, Z., Minasov, G., Kiryukhina, O., Jedrzejczak, R., 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: 37.44 kDa 
• Atom Count: 2,659 
• Modeled Residue Count: 295 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo0325 protein	A	306	Listeria monocytogenes EGD-e	Mutation(s): 0  Gene Names: lmo0325
UniProt
Find proteins for Q8YA39 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8YA39  Go to UniProtKB:  Q8YA39

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	C [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

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

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	B	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.199 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.31	α = 90
b = 103.93	β = 90
c = 112.81	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-07 
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Minasov, G., Kiryukhina, O., Jedrzejczak, R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2015-01-07
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-11-27
  Changes: Data collection, Database references, Structure summary