3FCA | pdb_00003fca

Genetic Incorporation of a Metal-ion Chelating Amino Acid into proteins as biophysical probe

• PDB DOI: https://doi.org/10.2210/pdb3FCA/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-21 Released: 2009-02-17 
• Deposition Author(s): Wang, F., Lee, H., Spraggon, G., Schultz, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.244 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Genetic incorporation of a metal-ion chelating amino acid into proteins as a biophysical probe.

Lee, H.S., Spraggon, G., Schultz, P.G., Wang, F.

(2009) J Am Chem Soc 131: 2481-2483

• PubMed: 19193005 
• DOI: https://doi.org/10.1021/ja808340b
• Primary Citation Related Structures: 
  3FCA


• PubMed Abstract: 
  

  A metal-ion chelating amino acid, (8-hydroxyquinolin-3-yl)alanine, was genetically encoded in E. coli by an amber nonsense codon and corresponding orthogonal tRNA/aminoacyl-tRNA synthetase pair. The amino acid was incorporated into TM0665 protein, and the mutant protein was cocrystallized with Zn(2+) to determine the structure by SAD phasing. The structure showed a high occupancy of the heavy metal bound to the HQ-Ala residue, and the heavy metal provided excellent phasing power to determine the structure. This method also facilitates the de novo design of metalloproteins with novel structures and functions, including fluorescent sensors.

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Organizational Affiliation: 
• Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

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: 62.61 kDa 
• Atom Count: 4,542 
• Modeled Residue Count: 582 
• Deposited Residue Count: 582 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine synthase	A, B	291	Thermus thermophilus	Mutation(s): 0  EC: 2.5.1.47

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HQA	A, B	L-PEPTIDE LINKING	C12 H12 N2 O3		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.244 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.858	α = 90
b = 135.858	β = 90
c = 74.939	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASES	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Wang, F., Lee, H., Spraggon, G., Schultz, P.G.

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-03-27
  Changes: Derived calculations