6SRT | pdb_00006srt

Endolysine N-acetylmuramoyl-L-alanine amidase LysCS from Clostridium intestinale URNW

• PDB DOI: https://doi.org/10.2210/pdb6SRT/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium intestinale URNW
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-09-06 Released: 2020-09-30 
• Deposition Author(s): Hakansson, M., Al-Karadaghi, S., Plotka, M., Kaczorowska, A.-K., Kaczorowski, T.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 
  0.157 (Depositor), 0.120 (DCC) 
• R-Value Work: 
  0.119 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.121 (Depositor) 

Starting Model: experimental

Literature

Structure and function of endolysines LysCS, LysC from Clostridium intestinale

Plotka, M., Hakansson, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 19.84 kDa 
• Atom Count: 1,543 
• Modeled Residue Count: 152 
• Deposited Residue Count: 169 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylmuramoyl-L-alanine amidase	A	169	Clostridium intestinale URNW	Mutation(s): 0  Gene Names: CINTURNW_1763
UniProt
Find proteins for U2NM08 (Clostridium intestinale URNW) Explore U2NM08  Go to UniProtKB:  U2NM08

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free:  0.157 (Depositor), 0.120 (DCC) 
• R-Value Work:  0.119 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.121 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.34	α = 90
b = 53.98	β = 90
c = 77	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Hakansson, M., Al-Karadaghi, S., Plotka, M., Kaczorowska, A.-K., Kaczorowski, T.

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Funding Organization	Location	Grant Number
European Research Council	Sweden	685778

Revision History  

• Version 1.0: 2020-09-30
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description