3A8S | pdb_00003a8s

Crystal structure analysis of the fluorescent protein KillerRed

PDB DOI: https://doi.org/10.2210/pdb3A8S/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Anthomedusae sp. DC-2005
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-10-08 Released: 2010-04-14
Deposition Author(s): Sakai, N., Kitago, Y., Takemoto, K., Matsuda, T., Nagai, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.298 (Depositor), 0.292 (DCC)
R-Value Work:
0.245 (Depositor), 0.244 (DCC)
R-Value Observed:
0.247 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3A8S

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

Literature

Crystal structure analysis of the fluorescent protein KillerRed

Sakai, N., Takemoto, K., Matsuda, T., Kitago, Y., Ayabe, T., Nagai, T.

To be published.

Macromolecule Content

Total Structure Weight: 53.39 kDa
Atom Count: 3,546
Modeled Residue Count: 442
Deposited Residue Count: 476
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KillerRed	A, B	238	Anthomedusae sp. DC-2005	Mutation(s): 1
UniProt
Find proteins for Q2TCH5 (Anthomedusae sp. DC-2005) Explore Q2TCH5 Go to UniProtKB: Q2TCH5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2TCH5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRQ Query on CRQ	A, B	L-PEPTIDE LINKING	C₁₆ H₁₆ N₄ O₅		GLN, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.298 (Depositor), 0.292 (DCC)
R-Value Work: 0.245 (Depositor), 0.244 (DCC)
R-Value Observed: 0.247 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.464	α = 90
b = 123.464	β = 90
c = 110.171	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
SHELXDE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-04-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-04-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2024-11-20
Changes: Structure summary
Version 3.0: 2026-03-18
Changes: Polymer sequence

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.