8DJ8 | pdb_00008dj8

Crystal Structure of Calgreen 1 protein

• PDB DOI: https://doi.org/10.2210/pdb8DJ8/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Corynactis californica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-06-30 Released: 2023-07-05 
• Deposition Author(s): Hung, L.-W., Nguyen, H.B., Waldo, G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Structure and Function of Engineered Variants of GFP-type Green Fluorescent protein from Corynactis californica (tentative)

Nguyen, H.B., Hung, L.-W., Waldo, G.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.1 kDa 
• Atom Count: 1,871 
• Modeled Residue Count: 211 
• Deposited Residue Count: 219 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calgreen One	A	219	Corynactis californica	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
C12	A	L-PEPTIDE LINKING	C15 H18 N3 O5		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.156	α = 90
b = 81.156	β = 90
c = 84.977	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Hung, L.-W., Nguyen, H.B., Waldo, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection, Derived calculations
• Version 2.0: 2024-07-10
  Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-11-13
  Changes: Structure summary