7BNG | pdb_00007bng

Complex structure of SH3b domain with L-canavanine

• PDB DOI: https://doi.org/10.2210/pdb7BNG/pdb

• Classification: CELL ADHESION
• Organism(s): Staphylococcus simulans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-01-22 Released: 2021-02-17 
• Deposition Author(s): Malecki, P.H., Sabala, I.
• Funding Organization(s): Foundation for Polish Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Complex structure of SH3b domain with L-canavanine

Malecki, P.H., Sabala, I.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.48 kDa 
• Atom Count: 1,858 
• Modeled Residue Count: 192 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysostaphin	A, B	96	Staphylococcus simulans	Mutation(s): 0  Gene Names: HMPREF3215_01322 EC: 3.4.24.75

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GGB (Subject of Investigation/LOI)	D [auth A]	L-CANAVANINE C5 H12 N4 O3 FSBIGDSBMBYOPN-VKHMYHEASA-N
SO4	F [auth A], G [auth A], H [auth A], I [auth A], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.898	α = 90
b = 55.232	β = 93.41
c = 48.994	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Malecki, P.H., Sabala, I.

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Funding Organization	Location	Grant Number
Foundation for Polish Science	Poland	POIR.04.04.00-00-3D8D/16-00

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references
• Version 2.1: 2024-01-31
  Changes: Refinement description