9D91 | pdb_00009d91

Crystal structure of L-asparaginase from Streptococcus pneumoniae TIGR4

• PDB DOI: https://doi.org/10.2210/pdb9D91/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-20 Released: 2024-10-09 
• Deposition Author(s): Gade, P., Endres, M., Babnigg, G., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)
• 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: 1.62 Å
• R-Value Free: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of L-asparaginase from Streptococcus pneumoniae TIGR4

Gade, P., Endres, M., Babnigg, G., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 35.42 kDa 
• Atom Count: 2,660 
• Modelled Residue Count: 314 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Asparaginase	A	320	Streptococcus pneumoniae	Mutation(s): 0  Gene Names:  ansB, A5N45_01685, AZJ70_05345, AZK02_05425, ERS019316_00818, ERS019420_01259, ERS021218_01180, GM536_02705, GM543_02955, GM545_09810, RLD18_05820, SAMEA3171064_00528, SAMEA3353485_02125, SAMEA3353631_01742, SAMEA3354366_01577, SAMEA3389353_01902, SAMEA4038883_00005 EC: 3.5.1.1
UniProt
Find proteins for A0A0H2ZNF4 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore A0A0H2ZNF4  Go to UniProtKB:  A0A0H2ZNF4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.369	α = 90
b = 74.016	β = 90
c = 132.655	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Gade, P., Endres, M., Babnigg, G., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)

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

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release