3SVE | pdb_00003sve

Engineered low-affinity halide-binding protein derived from YFP: bromide complex

• PDB DOI: https://doi.org/10.2210/pdb3SVE/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: 1.49 Å
• R-Value Free: 
  0.179 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.154 (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: 29.6 kDa 
• Atom Count: 2,150 
• Modeled Residue Count: 229 
• 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): 5  Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	B [auth A], C [auth A], D [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-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: 1.49 Å
• R-Value Free:  0.179 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.296	α = 90
b = 62.212	β = 90
c = 69.549	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	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: 2024-10-09
  Changes: Structure summary
• Version 3.0: 2026-03-18
  Changes: Polymer sequence