4YVB | pdb_00004yvb

Structure of D128N streptavidin

• PDB DOI: https://doi.org/10.2210/pdb4YVB/pdb

• Classification: Biotin binding protein
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-03-19 Released: 2016-03-23 
• Deposition Author(s): Baugh, L., Le Trong, I., Stayton, P.S., Stenkamp, R.E., Lybrand, T.P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.129 (Depositor) 

Starting Model: experimental

Literature

A Streptavidin Binding Site Mutation Yields an Unexpected Result

Baugh, L., Le Trong, I., Stayton, P.S., Stenkamp, R.E., Lybrand, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 51.75 kDa 
• Atom Count: 4,141 
• Modeled Residue Count: 477 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D	120	Streptomyces avidinii	Mutation(s): 1
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTN	E [auth A], F [auth B], G [auth C], H [auth D]	BIOTIN C10 H16 N2 O3 S YBJHBAHKTGYVGT-ZKWXMUAHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.597	α = 90
b = 98.95	β = 112.58
c = 52.638	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Baugh, L., Le Trong, I., Stayton, P.S., Stenkamp, R.E., Lybrand, T.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM080214

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description