8UQQ | pdb_00008uqq

Structure of mCLIFY: a circularly permuted yellow fluorescent protein

• PDB DOI: https://doi.org/10.2210/pdb8UQQ/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-10-24 Released: 2024-10-30 
• Deposition Author(s): Shweta, H., Gupta, K., Zhou, Y., Cui, X., Li, S., Lu, Z., Goldman, Y.E., Dantzig, J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), Other government, National Science Foundation (NSF, United States), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Structure of mCLIFY: a circularly permuted yellow fluorescent protein

Shweta, H., Gupta, K., Zhou, Y., Cui, X., Li, S., Lu, Z., Goldman, Y.E., Dantzig, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.17 kDa 
• Atom Count: 1,942 
• Modeled Residue Count: 224 
• Deposited Residue Count: 251 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mCLIFY	A	251	Aequorea victoria	Mutation(s): 0
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2	A	L-PEPTIDE LINKING	C13 H13 N3 O4		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.02	α = 90
b = 69.956	β = 90
c = 84.671	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Shweta, H., Gupta, K., Zhou, Y., Cui, X., Li, S., Lu, Z., Goldman, Y.E., Dantzig, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35-GM118139
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK125521
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM055560
Other government	United States	NIH S10 instrumentation grant: S10OD021573
National Science Foundation (NSF, United States)	United States	CMMI: 15-48571
Other private	United States	Johnson Research Foundation
Other government	United States	NIH S10 instrumentation grant: S10OD030413

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release