5LUR | pdb_00005lur

An avidin mutant

• PDB DOI: https://doi.org/10.2210/pdb5LUR/pdb

• Classification: biotin binding protein
• Organism(s): Gallus gallus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2016-09-09 Released: 2017-09-20 
• Deposition Author(s): Agrawal, N., Lehtonen, S.I., Riihimaki, T.A., Kulomaa, M.S., Hytonen, V.P., Johnson, M.S., Airenne, T.T.
• Funding Organization(s): Academy of Finland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

An avidin mutant

Agrawal, N., Lehtonen, S.I., Riihimaki, T.A., Kulomaa, M.S., Hytonen, V.P., Johnson, M.S., Airenne, T.T.

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: 32.39 kDa 
• Atom Count: 1,931 
• Modeled Residue Count: 232 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Avidin	A, B	138	Gallus gallus	Mutation(s): 12  Gene Names: AVD
UniProt
Find proteins for P02701 (Gallus gallus) Explore P02701  Go to UniProtKB:  P02701

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STR	C [auth A], D [auth B]	PROGESTERONE C21 H30 O2 RJKFOVLPORLFTN-LEKSSAKUSA-N
CL	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.13	α = 90
b = 80.35	β = 90
c = 43.42	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-09-20 
Deposition Author(s): Agrawal, N., Lehtonen, S.I., Riihimaki, T.A., Kulomaa, M.S., Hytonen, V.P., Johnson, M.S., Airenne, T.T.

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Funding Organization	Location	Grant Number
Academy of Finland	Finland	257814,272283,136288,290506

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary