2GSI | pdb_00002gsi

Crystal Structure of a Murine Fab in Complex with an 11 Residue Peptide Derived from Staphylococcal Nuclease

• PDB DOI: https://doi.org/10.2210/pdb2GSI/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Staphylococcus aureus
• Mutation(s): No 


• Deposited: 2006-04-26 Released: 2006-05-16 
• Deposition Author(s): Armstrong, A.A., Amzel, L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.293 (Depositor) 
• R-Value Work: 
  0.221 (Depositor) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of a Murine Fab in Complex with an 11 Residue Peptide Derived from Staphylococcal Nuclease

Armstrong, A.A., Amzel, L.M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

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

Biological Assembly 4  

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

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

Macromolecule Content 

• Total Structure Weight: 194.53 kDa 
• Atom Count: 13,426 
• Modeled Residue Count: 1,752 
• Deposited Residue Count: 1,788 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin (kappa) light chain	A, C, E, G	215	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin (gamma) heavy chain (VH + CH1 fragment)	B, D, F, H	221	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q6PF95 (Mus musculus) Explore Q6PF95  Go to UniProtKB:  Q6PF95

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermonuclease	I [auth X], J [auth Z], K [auth W], L [auth Y]	11	N/A	Mutation(s): 0  EC: 3.1.31.1
UniProt
Find proteins for P00644 (Staphylococcus aureus) Explore P00644  Go to UniProtKB:  P00644

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	M [auth B], N [auth D], O [auth E], P [auth F], Q [auth G], R [auth G], S [auth W]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free:  0.293 (Depositor) 
• R-Value Work:  0.221 (Depositor) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.739	α = 90
b = 131.04	β = 90
c = 291.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-16 
Deposition Author(s): Armstrong, A.A., Amzel, L.M.

Revision History  

• Version 1.0: 2006-05-16
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-10-05
  Changes: Derived calculations
• Version 1.4: 2019-11-20
  Changes: Derived calculations
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.6: 2024-11-20
  Changes: Structure summary