4GF6 | pdb_00004gf6

crystal structure of GFP with cuprum bound at the Incorporated metal Chelating Amino Acid PYZ151

• PDB DOI: https://doi.org/10.2210/pdb4GF6/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-08-03 Released: 2012-08-29 
• Deposition Author(s): Dong, J., Liu, X., Li, J., Wang, J., Gong, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.179 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Genetic incorporation of a metal-chelating amino Acid as a probe for protein electron transfer.

Liu, X., Li, J., Dong, J., Hu, C., Gong, W., Wang, J.

(2012) Angew Chem Int Ed Engl 51: 10261-10265

• PubMed: 22936654 
• DOI: https://doi.org/10.1002/anie.201204962
• Primary Citation Related Structures: 
  4GES, 4GF6

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Organizational Affiliation: 
• Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China.

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: 27.79 kDa 
• Atom Count: 2,304 
• Modeled Residue Count: 243 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
green fluorescent protein	A [auth B]	246	Aequorea victoria	Mutation(s): 3  Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	B	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CA	C [auth B], D [auth B], E [auth B], F [auth B], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0WZ	A [auth B]	L-PEPTIDE LINKING	C12 H13 N3 O3		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.179 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.827	α = 90
b = 63.052	β = 90
c = 70.369	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Dong, J., Liu, X., Li, J., Wang, J., Gong, W.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2012-10-24
  Changes: Database references
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection