8YDO

Crystal structure of dKeima570

• PDB DOI: https://doi.org/10.2210/pdb8YDO/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Montipora sp. 20
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-02-21 Released: 2024-04-03 
• Deposition Author(s): Nam, K.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.200 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Literature

Crystal structure of dKeima570

Nam, K.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 100.02 kDa 
• Atom Count: 7,483 
• Modelled Residue Count: 872 
• Deposited Residue Count: 880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Large stokes shift fluorescent protein	A, B, C, D	220	Montipora sp. 20	Mutation(s): 1  Gene Names: dkeima570
UniProt
Find proteins for Q1JU63 (Montipora sp. 20) Explore Q1JU63  Go to UniProtKB:  Q1JU63

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GYC	A, B, C, D	L-PEPTIDE LINKING	C14 H15 N3 O4 S		CYS, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.200 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.713	α = 90
b = 83.713	β = 90
c = 103.314	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Nam, K.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017R1D1A1B03033087
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017M3A9F6029736

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release