2XD5 | pdb_00002xd5

Structural insights into the catalytic mechanism and the role of Streptococcus pneumoniae PBP1b

• PDB DOI: https://doi.org/10.2210/pdb2XD5/pdb
• Entry: 2XD5 supersedes: 2JCI

• Classification: TRANSFERASE
• Organism(s): Streptococcus pneumoniae R6
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2010-04-29 Released: 2010-05-26 
• Deposition Author(s): Macheboeuf, P., Lemaire, D., Jamin, M., Dideberg, O., Dessen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structural Insights Into the Catalytic Mechanism and the Role of Streptococcus Pneumoniae Pbp1B

Macheboeuf, P., Lemaire, D., Jamin, M., Dideberg, O., Dessen, A.

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)

Macromolecule Content 

• Total Structure Weight: 108.94 kDa 
• Atom Count: 7,547 
• Modeled Residue Count: 937 
• Deposited Residue Count: 988 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PENICILLIN-BINDING PROTEIN 1B	A, B	494	Streptococcus pneumoniae R6	Mutation(s): 3  EC: 2.3.2 (PDB Primary Data), 2.4.1.129 (PDB Primary Data)
UniProt
Find proteins for Q7CRA4 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q7CRA4  Go to UniProtKB:  Q7CRA4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S2D	D [auth A], H [auth B]	N-BENZOYL-D-ALANINE C10 H11 N O3 UAQVHNZEONHPQG-SSDOTTSWSA-N
SO4	C [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.8	α = 90
b = 101.1	β = 90
c = 145	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-26 
Deposition Author(s): Macheboeuf, P., Lemaire, D., Jamin, M., Dideberg, O., Dessen, A.
• This entry supersedes: 2JCI

Revision History  

• Version 1.0: 2010-05-26
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary