7EZZ | pdb_00007ezz

Crystal structure of Salmonella typhi outer membrane phospholipase (OMPLA) dimer with bound calcium

• PDB DOI: https://doi.org/10.2210/pdb7EZZ/pdb
• Entry: 7EZZ supersedes: 5DQX

• Classification: HYDROLASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhi
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2021-06-02 Released: 2021-06-23 
• Deposition Author(s): Perumal, P., Raina, R., Sreeshma, N.S., Arockiasamy, A., Sundarabaalaji, N.
• Funding Organization(s): Department of Biotechnology (DBT, India), Department of Science & Technology (DST, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 
  0.272 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Salmonella typhi outer membrane phospholipase (OMPLA) dimer with bound calcium

Perumal, P., Raina, R., Sreeshma, N.S., Arockiasamy, A., Sundarabaalaji, N.

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)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 60.72 kDa 
• Atom Count: 4,237 
• Modeled Residue Count: 511 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A1	A, B	257	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0  Gene Names: pldA, STY3602, t3340 EC: 3.1.1.32 (PDB Primary Data), 3.1.1.4 (PDB Primary Data) Membrane Entity: Yes
UniProt
Find proteins for P0A232 (Salmonella typhi) Explore P0A232  Go to UniProtKB:  P0A232

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	C [auth A], D [auth A], E [auth A], G [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
D12 (Subject of Investigation/LOI)	H [auth A], I [auth B]	DODECANE C12 H26 SNRUBQQJIBEYMU-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	F [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free:  0.272 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.584	α = 90
b = 83.448	β = 90
c = 95.644	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
autoPROC	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): Perumal, P., Raina, R., Sreeshma, N.S., Arockiasamy, A., Sundarabaalaji, N.
• This entry supersedes: 5DQX

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/PR13735/BRB/10/786/2011 and BT/PR28080/BID/7/836/2018.
Department of Science & Technology (DST, India)	India	PDF/2016/003347
Department of Biotechnology (DBT, India)	India	BT/PR8636/BRB/10/530/2007
Department of Biotechnology (DBT, India)	India	BT/PR10275/GBD/27/88/2007

Revision History  

• Version 1.0: 2021-06-23
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Advisory, Data collection, Database references, Refinement description