8YKT | pdb_00008ykt

Fab and SEB complex

• PDB DOI: https://doi.org/10.2210/pdb8YKT/pdb

• Classification: PROTEIN BINDING/IMMUNE SYSTEM
• Organism(s): Staphylococcus aureus, Homo sapiens
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2024-03-05 Released: 2025-03-12 
• Deposition Author(s): Zeng, H., Fan, H.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Models: experimental

Literature

Structure of Staphylococcal Enterotoxin B mutant in complex with a neutralization antibody Fab fragment

Fan, H.Y., Zeng, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 76.03 kDa 
• Atom Count: 5,578 
• Modeled Residue Count: 661 
• Deposited Residue Count: 688 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enterotoxin type B	A	239	Staphylococcus aureus	Mutation(s): 0  Gene Names: entB
UniProt
Find proteins for P01552 (Staphylococcus aureus) Explore P01552  Go to UniProtKB:  P01552

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Heavy chain	B [auth H]	232	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Light chain	C [auth L]	217	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.25	α = 90
b = 73.32	β = 91.66
c = 114.22	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Zeng, H., Fan, H.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32070941
National Natural Science Foundation of China (NSFC)	China	32270989

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release