9J7R | pdb_00009j7r

Crystal structure of S. aureus MccB mutant K196A

• PDB DOI: https://doi.org/10.2210/pdb9J7R/pdb

• Classification: LYASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-08-19 Released: 2025-09-03 
• Deposition Author(s): Ha, N.-C., Lee, D., Lee, H., Byun, K.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of S. aureus MccB mutant K196A

Ha, N.-C., Lee, D., Lee, H., Byun, K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 83.41 kDa 
• Atom Count: 5,700 
• Modeled Residue Count: 723 
• Deposited Residue Count: 762 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-synthase homolog	A, B	381	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 1  Gene Names: yrhB, SAV0460 EC: 4.4.1.1
UniProt
Find proteins for A0A0H3JQ19 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JQ19  Go to UniProtKB:  A0A0H3JQ19

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGU (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid C13 H19 N2 O9 P JMRKOGDJNHPMHS-JTQLQIEISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.998	α = 90
b = 154.454	β = 90
c = 150.038	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Ha, N.-C., Lee, D., Lee, H., Byun, K.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	RS-2021-IP321036
National Research Foundation (NRF, Korea)	Korea, Republic Of	2022R1A2C109178313

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release