4DKM | pdb_00004dkm

Crystal Structure of Amphioxus GFPc1a

• PDB DOI: https://doi.org/10.2210/pdb4DKM/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Branchiostoma floridae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-02-03 Released: 2013-05-15 
• Deposition Author(s): Deheyn, D.D., Bomati, E.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.320 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.293 (Depositor), 0.300 (DCC) 

Starting Model: experimental

Literature

Fluorescent proteins in Amphioxus have strickingly different brightness, yet only few (but key) molecular differences

Bomati, E.K., Haley, J.E., Noel, J.P., Deheyn, D.D.

To be published.

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)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 189.21 kDa 
• Atom Count: 13,957 
• Modeled Residue Count: 1,712 
• Deposited Residue Count: 1,712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amphioxus Green Fluorescent Protein, GFPc1a	A, B, C, D, E, F, G, H	214	Branchiostoma floridae	Mutation(s): 1  Gene Names: BRAFLDRAFT_75523
UniProt
Find proteins for C3YRA3 (Branchiostoma floridae) Explore C3YRA3  Go to UniProtKB:  C3YRA3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.320 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.293 (Depositor), 0.300 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.76	α = 90
b = 130.46	β = 128.39
c = 106.33	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-15 
Deposition Author(s): Deheyn, D.D., Bomati, E.K.

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-20
  Changes: Structure summary