9PYL | pdb_00009pyl

Crystal structure of Zn(II)-bound ZETA_2

• PDB DOI: https://doi.org/10.2210/pdb9PYL/pdb

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


• Deposited: 2025-08-07 Released: 2025-10-29 
• Deposition Author(s): Bera, A.K., Kim, D., Woodbury, S., Kang, A., Baker, D.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.295 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: in silico

Literature

Computational Design of Metallohydrolases

Kim, D., Woodbury, S., Bera, A.K., Baker, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.97 kDa 
• Atom Count: 2,075 
• Modeled Residue Count: 247 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZETA_2	A, B	126	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.295 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.705	α = 90
b = 52.625	β = 90
c = 98.861	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Bera, A.K., Kim, D., Woodbury, S., Kang, A., Baker, D.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Science Foundation (NSF, United States)	United States	DGE-2140004

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release