2G5L | pdb_00002g5l

Streptavidin in complex with Nanotag

• PDB DOI: https://doi.org/10.2210/pdb2G5L/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-02-23 Released: 2007-02-06 
• Deposition Author(s): Perbandt, M., Bruns, O., Vallazza, M., Lamla, T., Betzel, C., Erdmann, V.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.172 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

High resolution structure of Streptavidin in complex with a novel high affinity peptide tag mimicking the biotin binding motif

Perbandt, M., Bruns, O., Vallazza, M., Lamla, T., Betzel, C., Erdmann, V.A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A4B1C1D1E1 

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

Macromolecule Content 

• Total Structure Weight: 28.63 kDa 
• Atom Count: 2,246 
• Modeled Residue Count: 240 
• Deposited Residue Count: 268 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B	127	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
(FME)(ASP)(VAL)(GLU)(ALA)(TRP)(LEU)	C [auth X], D [auth Y]	7	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	C [auth X], D [auth Y]	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.172 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.488	α = 90
b = 81.563	β = 90
c = 85.749	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-06 
Deposition Author(s): Perbandt, M., Bruns, O., Vallazza, M., Lamla, T., Betzel, C., Erdmann, V.A.

Revision History  

• Version 1.0: 2007-02-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary