7F87 | pdb_00007f87

Crystal structure of housekeeping sortase SrtA bound with self derived tripeptide from Lactobacillus rhamnosus GG

• PDB DOI: https://doi.org/10.2210/pdb7F87/pdb

• Classification: TRANSFERASE
• Organism(s): Lacticaseibacillus rhamnosus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-07-01 Released: 2022-07-06 
• Deposition Author(s): Pratap, S., Krishnan, V.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of housekeeping sortase SrtA bound with self derived tripeptide from Lactobacillus rhamnosus GG

Pratap, S., Krishnan, V.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.69 kDa 
• Atom Count: 2,442 
• Modeled Residue Count: 296 
• Deposited Residue Count: 304 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class A sortase	A, B	149	Lacticaseibacillus rhamnosus	Mutation(s): 0  Gene Names: F5976_12260, F8M46_11135, FEZ43_04140, GKD16_09085, HWN39_00700, LRHP540_01088, PY91_04000
UniProt
Find proteins for A0A0E3D3H8 (Lacticaseibacillus rhamnosus) Explore A0A0E3D3H8  Go to UniProtKB:  A0A0E3D3H8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Self Derived Peptide	C [auth F], D [auth G]	3	Lacticaseibacillus rhamnosus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.608	α = 90
b = 55.674	β = 103.22
c = 75.312	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-06 
Deposition Author(s): Pratap, S., Krishnan, V.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/PR5891/BRB/10/1098/2012

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary