9S09 | pdb_00009s09

300 ns Intermediate-state of CBD of TtCarH at 30 mJ/cm2 laser fluence (TR-SFX, SACLA), refined against extrapolated structure factors

PDB DOI: https://doi.org/10.2210/pdb9S09/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Thermus thermophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-07-16 Released: 2026-01-28
Deposition Author(s): Rios-Santacruz, R., Coquelle, N., Colletier, J.P., De Zitter, E., Schiro, G., Weik, M.
Funding Organization(s): Agence Nationale de la Recherche (ANR), Centre National de la Recherche Scientifique (CNRS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.328 (Depositor), 0.330 (DCC)
R-Value Work:
0.277 (Depositor), 0.277 (DCC)
R-Value Observed:
0.279 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Integrated structural dynamics uncover new modes of B12 photoreceptor activation

Rios-Santacruz, R., Coquelle, N., Colletier, J.P., De Zitter, E., Schiro, G., Weik, M.

(2026) Nature

DOI: https://doi.org/10.1038/s41586-025-10074-2

Macromolecule Content

Total Structure Weight: 99.37 kDa
Atom Count: 6,667
Modeled Residue Count: 786
Deposited Residue Count: 860
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcriptional regulator	A, B, C, D	215	Thermus thermophilus	Mutation(s): 0 Gene Names: TT_P0056
UniProt
Find proteins for Q746J7 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q746J7 Go to UniProtKB: Q746J7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q746J7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 (Subject of Investigation/LOI) Query on B12 Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
5AD (Subject of Investigation/LOI) Query on 5AD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain G [auth B]	E [auth A], G [auth B], I [auth C], K [auth D]	5'-DEOXYADENOSINE C₁₀ H₁₃ N₅ O₃ XGYIMTFOTBMPFP-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.328 (Depositor), 0.330 (DCC)
R-Value Work: 0.277 (Depositor), 0.277 (DCC)
R-Value Observed: 0.279 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.8	α = 90
b = 71.08	β = 90
c = 207.27	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2026-01-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	PhotoGene
Centre National de la Recherche Scientifique (CNRS)	France	GoToXFEL
Agence Nationale de la Recherche (ANR)	France	BioXFEL