3SVC | pdb_00003svc

Engineered medium-affinity halide-binding protein derived from YFP: chloride complex

• PDB DOI: https://doi.org/10.2210/pdb3SVC/pdb

• Classification: HALIDE BINDING PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-07-12 Released: 2012-07-18 
• Deposition Author(s): Wang, W., Grimley, J.S., Beese, L.S., Hellinga, H.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Determination of engineered chloride-binding site structures in fluorescent proteins reveals principles of halide recognition

Wang, W., Grimley, J.S., Augustine, G.J., Beese, L.S., Hellinga, H.W.

To be published.

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: 29.48 kDa 
• Atom Count: 2,226 
• Modeled Residue Count: 230 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	258	Aequorea victoria	Mutation(s): 7  Gene Names: GFP
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
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.31 Å
• R-Value Free:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.615	α = 90
b = 62.664	β = 90
c = 65.951	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-18 
Deposition Author(s): Wang, W., Grimley, J.S., Beese, L.S., Hellinga, H.W.

Revision History  

• Version 1.0: 2012-07-18
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 2.1: 2024-11-20
  Changes: Structure summary