2FFF | pdb_00002fff

Open Form of a Class A Transpeptidase Domain

• PDB DOI: https://doi.org/10.2210/pdb2FFF/pdb

• Classification: MEMBRANE PROTEIN, TRANSFERASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-12-19 Released: 2006-06-20 
• Deposition Author(s): Lovering, A.L., Strynadka, N.C.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 
  0.246 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of an "open" form of PBP1B from Streptococcus pneumoniae.

Lovering, A.L., De Castro, L., Lim, D., Strynadka, N.C.

(2006) Protein Sci 15: 1701-1709

• PubMed: 16751607 
• DOI: https://doi.org/10.1110/ps.062112106
• Primary Citation Related Structures: 
  2FFF


• PubMed Abstract: 
  

  The class A PBP1b from Streptococcus pneumoniae is responsible for glycosyltransferase and transpeptidase (TP) reactions, forming the peptidoglycan of the bacterial cell wall. The enzyme has been produced in a stable, soluble form and undergoes time-dependent proteolysis to leave an intact TP domain. Crystals of this TP domain were obtained, diffracting to 2.2 A resolution, and the structure was solved by using molecular replacement. Analysis of the structure revealed an "open" active site, with important conformational differences to the previously determined "closed" apoenzyme. The active-site nucleophile, Ser460, is in an orientation that allows for acylation by beta-lactams. Consistent with the productive conformation of the conserved active-site catalytic residues, adjacent loops show only minor deviation from those of known acyl-enzyme structures. These findings are discussed in the context of enzyme functionality and the possible conformational sampling of PBP1b between active and inactive states.

---

Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Center for Blood Research, University of British Columbia, Vancouver, Canada.

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: 51.5 kDa 
• Atom Count: 3,849 
• Modeled Residue Count: 468 
• Deposited Residue Count: 468 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
penicillin-binding protein 1B	A	15	Streptococcus pneumoniae	Mutation(s): 0
UniProt
Find proteins for Q4TUQ1 (Streptococcus pneumoniae) Explore Q4TUQ1  Go to UniProtKB:  Q4TUQ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
penicillin-binding protein 1B	B	453	Streptococcus pneumoniae	Mutation(s): 0
UniProt
Find proteins for O70038 (Streptococcus pneumoniae) Explore O70038  Go to UniProtKB:  O70038

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free:  0.246 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.661	α = 90
b = 78.043	β = 113.02
c = 60.315	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-20 
Deposition Author(s): Lovering, A.L., Strynadka, N.C.J.

Revision History  

• Version 1.0: 2006-06-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description