7VNS | pdb_00007vns

Sandercyanin mutant E79A-Biliverdin complex

PDB DOI: https://doi.org/10.2210/pdb7VNS/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Sander vitreus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-10-12 Released: 2022-05-25
Deposition Author(s): Yadav, K., Ghosh, S., Subramanian, R.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.177 (Depositor), 0.161 (DCC)
R-Value Work:
0.174 (Depositor)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Phenylalanine stacking enhances the red fluorescence of biliverdin IX alpha on UV excitation in sandercyanin fluorescent protein.

Yadav, K., Ghosh, S., Barak, A., Schaefer, W., Subramanian, R.

(2022) FEBS Lett 596: 796-805

PubMed: 35020202 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.14281
Primary Citation Related Structures:
7VNL, 7VNS

PubMed Abstract:
Biliverdin IXα (BV) binds to several prokaryotic and eukaryotic proteins. How nature exploits the versatility of BV's properties is not fully understood. Unlike free BV, the Sandercyanin fluorescent protein bound to BV (SFP-BV) shows enhanced red fluorescence (675 nm) on excitation in the UV region (380 nm). Site-directed mutagenesis showed that the BV complex of two SFP variants, F55A and E79A, resulted in the loss of red fluorescence. Crystal structures of the complexes of these proteins with BV show the absence of stacking interactions of the F55 phenyl ring with BV. BV changes from ZZZssa conformation in the wild-type to ZZZsss conformation in the variants. In the nonfluorescent mutants, the lowest excited state is destabilized, resulting in nonradiative decay.

Organizational Affiliation

Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.

Macromolecule Content

Total Structure Weight: 41.37 kDa
Atom Count: 3,060
Modeled Residue Count: 338
Deposited Residue Count: 366
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sandercyanin Fluorescent Protein	A, B	183	Sander vitreus	Mutation(s): 1
UniProt
Find proteins for A0A1D5B367 (Sander vitreus) Explore A0A1D5B367 Go to UniProtKB: A0A1D5B367
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1D5B367
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BLA (Subject of Investigation/LOI) Query on BLA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	BILIVERDINE IX ALPHA C₃₃ H₃₄ N₄ O₆ GWZYPXHJIZCRAJ-SRVCBVSDSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.177 (Depositor), 0.161 (DCC)
R-Value Work: 0.174 (Depositor)
R-Value Observed: 0.174 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.024	α = 90
b = 160.024	β = 90
c = 82.485	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-25

Deposition Author(s):

Subramanian, R.

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/PR5801/INF/22/156/2012

Revision History (Full details and data files)

Version 1.0: 2022-05-25
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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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.