1UW1 | pdb_00001uw1

A Novel ADP- and Zinc-binding fold from function-directed in vitro evolution

• PDB DOI: https://doi.org/10.2210/pdb1UW1/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-01-28 Released: 2004-03-26 
• Deposition Author(s): Lo Surdo, P., Walsh, M.A., Sollazzo, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 

Literature

A Novel Adp- and Zinc-Binding Fold from Function-Directed in Vitro Evolution

Lo Surdo, P., Walsh, M.A., Sollazzo, M.

(2004) Nat Struct Mol Biol 11: 382

• PubMed: 15024384 
• DOI: https://doi.org/10.1038/nsmb745
• Primary Citation of Related Structures:  
  1UW1


• PubMed Abstract: 
  

  A great challenge to biologists is to create proteins with novel folds and tailored functions. As an alternative to de novo protein design, we investigated the structure of a randomly generated protein targeted to bind ATP. The crystal structure reveals a novel alpha/beta fold bound to its ligand, representing both the first protein structure derived from in vitro evolution and the first nucleotide-binding protein stabilized by a zinc ion.

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Organizational Affiliation: 

Istituto di Ricerche di Biologia Molecolare (IRBM), Via Pontina Km 30.600, 00040 Pomezia, Roma, Italy. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 10.1 kDa 
• Atom Count: 695 
• Modelled Residue Count: 67 
• Deposited Residue Count: 80 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARTIFICIAL NUCLEOTIDE BINDING PROTEIN (ANBP)	A	80	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.077	α = 90
b = 71.077	β = 90
c = 54.883	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-26 
Deposition Author(s): Lo Surdo, P., Walsh, M.A., Sollazzo, M.

Revision History  

• Version 1.0: 2004-03-26
  Type: Initial release
  
• Version 1.1: 2015-10-21
  Changes: Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2019-05-15
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other