2BC3

T7-tagged full-length streptavidin

PDB DOI: https://doi.org/10.2210/pdb2BC3/pdb

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

Deposited: 2005-10-18 Released: 2005-10-25
Deposition Author(s): Stenkamp, R.E., Le Trong, I., Ward, T.R., Humbert, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.243
R-Value Work: 0.175
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystallographic Analysis of a Full-length Streptavidin with Its C-terminal Polypeptide Bound in the Biotin Binding Site.

Le Trong, I., Humbert, N., Ward, T.R., Stenkamp, R.E.

(2006) J Mol Biol 356: 738-745

PubMed: 16384581 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2005.11.086
Primary Citation of Related Structures:
2BC3

PubMed Abstract:
The structure of a full-length streptavidin has been determined at 1.7 A resolution and shows that the 20 residue extension at the C terminus forms a well-ordered polypeptide loop on the surface of the tetramer. Residues 150-153 of the extension are bound to the ligand-binding site, possibly competing with exogenous ligands. The binding mode of these residues is compared with that of biotin and peptidic ligands. The observed structure helps to rationalize the observations that full-length mature streptavidin binds biotinylated macromolecules with reduced affinity.

Organizational Affiliation

Departments of Biological Structure and Biochemistry and the Biomolecular Structure Center, University of Washington, Box 357420, Seattle, WA 98195-7420, USA.

Macromolecule Content

Total Structure Weight: 33.42 kDa
Atom Count: 2,434
Modelled Residue Count: 286
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B	159	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629 Go to UniProtKB: P22629
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B]	D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.243
R-Value Work: 0.175
R-Value Observed: 0.175
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.704	α = 90
b = 82.391	β = 103.48
c = 46.71	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	model building
SHELXL-97	refinement
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-10-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-10-25
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: 2022-12-21
Changes: Database references, Derived calculations
Version 1.4: 2024-04-03
Changes: Data collection, Refinement description