5DRF | pdb_00005drf

Green/cyan WasCFP-pH5.5 at pH 5.5

• PDB DOI: https://doi.org/10.2210/pdb5DRF/pdb

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


• Deposited: 2015-09-15 Released: 2016-07-27 
• Deposition Author(s): Pletnev, V.Z., Pletneva, N.V., Pletnev, S.V.
• Funding Organization(s): Russian Foundation for Basic Research, Molecular Cell Biology fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 
  0.165 (Depositor), 0.165 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of pH and T dependent green fluorescent protein WasCFP with Trp based chromophore

Pletnev, V.Z., Pletneva, N., Efremov, R.G., Goryacheva, E.A., Artemyev, I.V., Arkhipova, S.F., Sarkisyan, K.S., Mishin, A.S., Lukyanov, K.A., Pletnev, S.V.

(2016) Russ J Bioorg Chem 42 (6)

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: 28.17 kDa 
• Atom Count: 2,223 
• Modeled Residue Count: 228 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WasCFP-pH5.5 at pH 5.5	A	248	Aequorea coerulescens	Mutation(s): 0
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
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRF	A	L-PEPTIDE LINKING	C17 H18 N4 O4		THR, TRP, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free:  0.165 (Depositor), 0.165 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.994	α = 90
b = 51.289	β = 95.46
c = 47.94	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): Pletnev, V.Z., Pletneva, N.V., Pletnev, S.V.

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Funding Organization	Location	Grant Number
Russian Foundation for Basic Research	Russian Federation	14-04-00004
Molecular Cell Biology fund	Russian Federation	--

Revision History  

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Advisory, Author supporting evidence, Derived calculations
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary
• Version 2.0: 2026-03-18
  Changes: Polymer sequence