5TRO | pdb_00005tro

1.8 Angstrom Resolution Crystal Structure of Dimerization and Transpeptidase domains (residues 39-608) of Penicillin-Binding Protein 1 from Staphylococcus aureus.

• PDB DOI: https://doi.org/10.2210/pdb5TRO/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-10-26 Released: 2016-11-09 
• Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.209 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

1.8 Angstrom Resolution Crystal Structure of Dimerization and Transpeptidase domains (residues 39-608) of Penicillin-Binding Protein 1 from Staphylococcus aureus.

Minasov, G., Shuvalova, L., Kiryukhina, O., 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 129.69 kDa 
• Atom Count: 8,690 
• Modeled Residue Count: 1,011 
• Deposited Residue Count: 1,146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 1	A, B	573	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: pbp1, SACOL1194
UniProt
Find proteins for A0A0H2WVW5 (Staphylococcus aureus (strain COL)) Explore A0A0H2WVW5  Go to UniProtKB:  A0A0H2WVW5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.209 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35tro

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.843	α = 90
b = 72.202	β = 103.18
c = 86.362	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary