9J7Q | pdb_00009j7q

Crystal structure of S. aureus MccB with PLP

• PDB DOI: https://doi.org/10.2210/pdb9J7Q/pdb

• Classification: LYASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 1.64 Å
• R-Value Free: 
  0.201 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of S. aureus MccB with PLP

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: 41.95 kDa 
• Atom Count: 3,165 
• Modeled Residue Count: 380 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-synthase homolog	A	380	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: yrhB, SAV0460
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
PEG	B [auth A], C [auth A], D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.201 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.747	α = 90
b = 80.261	β = 90
c = 161.387	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