Macromolecule Content

Total Structure Weight: 54.29 kDa
Atom Count: 3860
Modelled Residue Count: 463
Deposited Residue Count: 512
Unique protein chains: 1

1SWG

CIRCULAR PERMUTED STREPTAVIDIN E51/A46 IN COMPLEX WITH BIOTIN

PDB DOI: 10.2210/pdb1SWG/pdb

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

Deposited: 1997-07-12 Released: 1998-07-15
Deposition Author(s): Freitag, S., Chu, V., Le Trong, I., Stayton, P.S., Stenkamp, R.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.245
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin-biotin system.

Chu, V., Freitag, S., Le Trong, I., Stenkamp, R.E., Stayton, P.S.

(1998) Protein Sci 7: 848-859

PubMed: 9568892 Search on PubMedSearch on PubMed Central
DOI: 10.1002/pro.5560070403
Primary Citation of Related Structures:
1SWF, 1SWG

PubMed Abstract:

A circularly permuted streptavidin (CP51/46) has been designed to remove the flexible polypeptide loop that undergoes an open to closed conformational change when biotin is bound. The original termini have been joined by a tetrapeptide linker, and four loop residues have been removed, resulting in the creation of new N- and C-termini. Isothermal titration calorimetric studies show that the association constant has been reduced approximately six orders of magnitude below that of wild-type streptavidin to 10(7) M(-1). The deltaH degrees of biotin association for CP51/46 is reduced by 11.1 kcal/mol. Crystal structures of CP51/46 and its biotin complex show no significant alterations in the binding site upon removal of the loop. A hydrogen bond between Ser45 and Ser52 found in the absence of biotin is broken in the closed conformation as the side-chain hydroxyl of Ser45 moves to hydrogen bond to a ureido nitrogen of biotin. This is true in both the wild-type and CP51/46 forms of the protein, and the hydrogen bonding interaction might thus help nucleate closure of the loop. The reduced entropic cost of binding biotin to CP51/46 is consistent with the removal of this loop and a reduction in entropic costs associated with loop closure and immobilization. The reduced enthalpic contribution to the free energy of binding is not readily explainable in terms of the molecular structure, as the binding contacts are nearly entirely conserved, and only small differences in solvent accessible surfaces are observed relative to wild-type streptavidin.

Related Citations:

Thermodynamic Consequences of the Deletion of a Flexible Loop by Circular Permutation in the Streptavidin-Biotin System
Chu, V., Freitag, S., Le Trong, I., Stenkamp, R.E., Stayton, P.S.
() To be published --: --

Structural Studies of the Streptavidin Binding Loop
Freitag, S., Le Trong, I., Klumb, L., Stayton, P.S., Stenkamp, R.E.
(1997) Protein Sci 6: 1157

Organizational Affiliation:

Department of Bioengineering, University of Washington, Seattle 98195-7962, USA.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46	A, B, C, D	128	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
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTN Query on BTN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	BIOTIN C₁₀ H₁₆ N₂ O₃ S YBJHBAHKTGYVGT-ZKWXMUAHSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
BTN	PDBBind: 1SWG	Kd: 43.9 (nM) from 1 assay(s)
	Binding MOAD: 1SWG	Kd: 43.9 (nM) from 1 assay(s)
	BindingDB: 1SWG	Kd: 1 (nM) from 1 assay(s)
	BindingDB: 1SWG	ΔH: min: -1.23e+2, max: -6.69e+1 (kJ/mol) from 12 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.245
R-Value Observed: 0.190
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.9	α = 90
b = 78.6	β = 90
c = 90.8	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 1997-07-12
Released Date: 1998-07-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1998-07-15
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance