5SBJ | pdb_00005sbj

The crystal structure of METP in complex with Cd at a resolution of 1.29 A.

• PDB DOI: https://doi.org/10.2210/pdb5SBJ/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., Pavone, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: in silico

Literature

Miniaturization process reloaded - structural and functional insights from a miniaturized rubredoxin

Chino, M., Di Costanzo, L.

To be published.

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: 3.07 kDa 
• Atom Count: 230 
• Modeled 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
CD (Subject of Investigation/LOI)	B [auth C]	CADMIUM ION Cd WLZRMCYVCSSEQC-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: 1.28 Å
• R-Value Free:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.07	α = 90
b = 56.654	β = 90
c = 19.331	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 

Deposition Data

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

Revision History  

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