8H1I | pdb_00008h1i

Crystal structure of PlyGRCS, a bacteriophage Endolysin in complex with Cold shock protein C

• PDB DOI: https://doi.org/10.2210/pdb8H1I/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Staphylococcus phage GRCS, Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-03 Released: 2023-10-18 
• Deposition Author(s): Padmanabhan, B., Gopinatha, K., Mandal, M., Saranya, G., Sudhagar, B.
• Funding Organization(s): Science and Engineering Research Board (SERB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of PlyGRCS, a bacteriophage Endolysin in complex with Cold shock protein C

Padmanabhan, B., Gopinatha, K., Mandal, M., Saranya, G., Sudhagar, B.

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)

Macromolecule Content 

• Total Structure Weight: 36.2 kDa 
• Atom Count: 2,770 
• Modeled Residue Count: 319 
• Deposited Residue Count: 319 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endolysin	A	250	Staphylococcus phage GRCS	Mutation(s): 0  Gene Names: GRCS_0015 EC: 3.5.1.28
UniProt
Find proteins for W6EBY7 (Staphylococcus phage GRCS) Explore W6EBY7  Go to UniProtKB:  W6EBY7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cold shock-like protein CspC	B	69	Escherichia coli K-12	Mutation(s): 0  Gene Names: cspC, msmB, b1823, JW1812
UniProt
Find proteins for P0A9Y6 (Escherichia coli (strain K12)) Explore P0A9Y6  Go to UniProtKB:  P0A9Y6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.667	α = 90
b = 55.29	β = 90
c = 99.308	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Padmanabhan, B., Gopinatha, K., Mandal, M., Saranya, G., Sudhagar, B.

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Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	CRG/2019/002603

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary