9XGD | pdb_00009xgd

Crystal structure of dKeima570 at pH 4.0

PDB DOI: https://doi.org/10.2210/pdb9XGD/pdb

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

Deposited: 2025-10-30 Released: 2026-11-04
Deposition Author(s): Nam, K.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.259 (Depositor), 0.264 (DCC)
R-Value Work:
0.209 (Depositor), 0.215 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9XGD

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of dKeima570 at pH 4.0

Nam, K.H.

To be published.

Macromolecule Content

Total Structure Weight: 50.01 kDa
Atom Count: 3,607
Modeled Residue Count: 434
Deposited Residue Count: 440
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	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

Non-standard Monomers 1 Unique
ID	Chains	Type	Formula	2D Diagram
GYC Query on GYC	A, B	L-PEPTIDE LINKING	C₁₄ H₁₅ N₃ O₄ S

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.259 (Depositor), 0.264 (DCC)
R-Value Work: 0.209 (Depositor), 0.215 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.584	α = 90
b = 84.584	β = 90
c = 105.296	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021R1I1A1A01050838

Revision History (Full details and data files)

Version 1.0: 2026-11-04
Type: Initial release