8YDO | pdb_00008ydo

Crystal structure of dKeima570

PDB DOI: https://doi.org/10.2210/pdb8YDO/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Montipora sp. 20
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-02-21 Released: 2024-04-03
Deposition Author(s): Nam, K.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.200 (Depositor), 0.207 (DCC)
R-Value Work:
0.162 (Depositor), 0.170 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8YDO

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of dKeima570

Nam, K.H.

To be published.

Macromolecule Content

Total Structure Weight: 100.02 kDa
Atom Count: 7,483
Modeled Residue Count: 872
Deposited Residue Count: 880
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Large stokes shift fluorescent protein	A, B, C, D	220	Montipora sp. 20	Mutation(s): 1 Gene Names: dkeima570
UniProt
Find proteins for Q1JU63 (Montipora sp. 20) Explore Q1JU63 Go to UniProtKB: Q1JU63
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1JU63
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GYC Query on GYC	A, B, C, D	L-PEPTIDE LINKING	C₁₄ H₁₅ N₃ O₄ S		CYS, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.200 (Depositor), 0.207 (DCC)
R-Value Work: 0.162 (Depositor), 0.170 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.713	α = 90
b = 83.713	β = 90
c = 103.314	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017R1D1A1B03033087
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017M3A9F6029736

Revision History (Full details and data files)

Version 1.0: 2024-04-03
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary
Version 2.0: 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.