9GA0 | pdb_00009ga0

XPA crystal grown in HEK293 cell

PDB DOI: https://doi.org/10.2210/pdb9GA0/pdb

Classification: LUMINESCENT PROTEIN
Organism(s): Dipsastraea favus
Mutation(s): Yes

Deposited: 2024-07-26 Released: 2025-08-27
Deposition Author(s): Melicher, F., Isabet, T., Chavas, L.M.G., Montaville, P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.235 (Depositor), 0.229 (DCC)
R-Value Work:
0.199 (Depositor), 0.196 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

1.6A in-vivo XPA crystal structure grown in HEK293 cell

Melicher, F., Isabet, T., Montaville, P., Chavas, L.M.G.

To be published.

Macromolecule Content

Total Structure Weight: 51.68 kDa
Atom Count: 4,178
Modeled Residue Count: 450
Deposited Residue Count: 452
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photoconvertible fluorescent protein	A [auth G], B [auth H]	226	Dipsastraea favus	Mutation(s): 1
UniProt
Find proteins for Q53UG8 (Dipsastraea favus) Explore Q53UG8 Go to UniProtKB: Q53UG8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q53UG8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth G] MOL2 format, chain C [auth G] mmCIF format, chain C [auth G]	C [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth G] Interactions & Density Focus chain C [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.235 (Depositor), 0.229 (DCC)
R-Value Work: 0.199 (Depositor), 0.196 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.003	α = 90
b = 84.322	β = 90
c = 118.348	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	France	--

Revision History (Full details and data files)

Version 1.0: 2025-08-27
Type: Initial release

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.