5JCV | pdb_00005jcv

Sortase B from Listeria monocytogenes.

• PDB DOI: https://doi.org/10.2210/pdb5JCV/pdb

• Classification: HYDROLASE
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-15 Released: 2016-04-27 
• Deposition Author(s): Osipiuk, J., Zhou, M., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 
  0.249 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Sortase B from Listeria monocytogenes.

Osipiuk, J., Zhou, M., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 21.89 kDa 
• Atom Count: 1,490 
• Modeled Residue Count: 175 
• Deposited Residue Count: 183 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo2181 protein	A	183	Listeria monocytogenes EGD-e	Mutation(s): 0  Gene Names: lmo2181 EC: 3.4.22
UniProt
Find proteins for Q8Y588 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y588  Go to UniProtKB:  Q8Y588

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free:  0.249 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35jcv

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.155	α = 90
b = 70.155	β = 90
c = 224.471	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
REFMAC	refinement
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-04-27 
Deposition Author(s): Osipiuk, J., Zhou, M., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272200700058C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History  

• Version 1.0: 2016-04-27
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Structure summary