5U47

1.95 Angstrom Resolution Crystal Structure of Penicillin Binding Protein 2X from Streptococcus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb5U47/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Streptococcus thermophilus LMG 18311
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-12-03 Released: 2016-12-28 
• Deposition Author(s): Minasov, G., Shuvalova, L., Cardona-Correa, A., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.210 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

1.95 Angstrom Resolution Crystal Structure of Penicillin Binding Protein 2X from Streptococcus thermophilus.

Minasov, G., Shuvalova, L., Cardona-Correa, A., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 76.93 kDa 
• Atom Count: 5,854 
• Modelled Residue Count: 684 
• Deposited Residue Count: 707 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin binding protein 2X	A	707	Streptococcus thermophilus LMG 18311	Mutation(s): 1  Gene Names: pbp2X, stu1701
UniProt
Find proteins for Q5M2U8 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M2U8  Go to UniProtKB:  Q5M2U8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.210 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/m35u47

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.535	α = 90
b = 78.494	β = 90
c = 164.856	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-28 
Deposition Author(s): Minasov, G., Shuvalova, L., Cardona-Correa, A., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-12-28
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary