5SBG

The crystal structure of METP in complex with Zn at a resolution of 1.34 A.

• PDB DOI: https://doi.org/10.2210/pdb5SBG/pdb
• Deposition Group: G_1002191 ExploreG_1002191

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2021-08-24 Released: 2023-02-15 
• Deposition Author(s): Di Costanzo, L., La Gatta, S., Chino, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.174 
• R-Value Work: 0.131 
• R-Value Observed: 0.133 

Literature

Designed Rubredoxin miniature in a fully artificial electron chain triggered by visible light

Chino, M., Di Costanzo, L.F., Leone, L., La Gatta, S., Famulari, A., Chiesa, M., Lombardi, A., Pavone, V.

(2023) Nat Commun 14: 2368

• DOI: https://doi.org/10.1038/s41467-023-37941-8

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 3.02 kDa 
• Atom Count: 238 
• Modelled Residue Count: 30 
• Deposited Residue Count: 30 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METP, miniaturized rubredoxin	A [auth C]	30	synthetic construct	Mutation(s): 0

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB	A [auth C]	L-PEPTIDE LINKING	C4 H9 N O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.174 
• R-Value Work: 0.131 
• R-Value Observed: 0.133 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.663	α = 90
b = 55.978	β = 90
c = 19.128	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Di Costanzo, L., La Gatta, S., Chino, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2023-05-17
  Changes: Database references
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-04-03
  Changes: Refinement description