5T1Q | pdb_00005t1q

2.15 Angstrom Crystal Structure of N-acetylmuramoyl-L-alanine Amidase from Staphylococcus aureus.

• PDB DOI: https://doi.org/10.2210/pdb5T1Q/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-08-19 Released: 2017-06-07 
• Deposition Author(s): Minasov, G., Nocadello, S., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Bagnoli, F., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Models: experimental

Literature

2.15 Angstrom Crystal Structure of N-acetylmuramoyl-L-alanine Amidase from Staphylococcus aureus.

Minasov, G., Nocadello, S., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Bagnoli, F., Grandi, G., 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)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 162.46 kDa 
• Atom Count: 12,199 
• Modeled Residue Count: 1,423 
• Deposited Residue Count: 1,436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979	A, B, C, D	359	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0  Gene Names: SAOUHSC_02979
UniProt
Find proteins for Q2G222 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G222  Go to UniProtKB:  Q2G222

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	J [auth C]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
NA	E [auth A], F [auth A], G [auth B], H [auth C], I [auth C], K [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35t1q

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.57	α = 108.7
b = 66.838	β = 104.72
c = 102.737	γ = 90.25

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: 2017-06-07 
Deposition Author(s): Minasov, G., Nocadello, S., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Bagnoli, F., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-10-23
  Changes: Structure summary