3SVB | pdb_00003svb

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

PDB DOI: https://doi.org/10.2210/pdb3SVB/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: 1.30 Å
R-Value Free:
0.164 (Depositor), 0.163 (DCC)
R-Value Work:
0.136 (Depositor), 0.132 (DCC)
R-Value Observed:
0.137 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3SVB

This is version 3.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 29.37 kDa
Atom Count: 2,229
Modeled Residue Count: 227
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42212
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2 Query on CR2	A	L-PEPTIDE LINKING	C₁₃ H₁₃ N₃ O₄		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.164 (Depositor), 0.163 (DCC)
R-Value Work: 0.136 (Depositor), 0.132 (DCC)
R-Value Observed: 0.137 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.914	α = 90
b = 63.194	β = 90
c = 69.229	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

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Entry History

Deposition Data

Released Date: 2012-07-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-07-18
Type: Initial release
Version 1.1: 2017-11-08
Changes: Advisory, Refinement description
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2024-10-30
Changes: Structure summary
Version 3.0: 2026-03-18
Changes: Polymer sequence

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.