5JEN | pdb_00005jen

Crystal structure of the anti-sigma factor RsiV bound to lysozyme

• PDB DOI: https://doi.org/10.2210/pdb5JEN/pdb

• Classification: HYDROLASE/HYDROLASE RECEPTOR
• Organism(s): Bacillus subtilis subsp. subtilis str. 168, Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-18 Released: 2016-09-07 
• Deposition Author(s): Gakhar, L., Williams, K.B., Ellermeir, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.237 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

The anti-sigma factor RsiV is a receptor for lysozyme: The crystal structure of RsiV-lysozyme complex

Hastie, J.L., Williams, K.B., Gakhar, L., Houtman, J.C., Ellermeier, C.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 92.51 kDa 
• Atom Count: 5,796 
• Modeled Residue Count: 673 
• Deposited Residue Count: 802 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-sigma-V factor RsiV	A, C	271	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: rsiV, yrhM, BSU27130
UniProt
Find proteins for O05403 (Bacillus subtilis (strain 168)) Explore O05403  Go to UniProtKB:  O05403

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	B, D	130	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	H [auth B], L [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], F [auth A], G [auth B], I [auth C], J [auth C], K [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, C	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:  0.237 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.213	α = 90
b = 130.326	β = 90
c = 136.712	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-07 
Deposition Author(s): Gakhar, L., Williams, K.B., Ellermeir, C.D.

Revision History  

• Version 1.0: 2016-09-07
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary