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- PDB-9s06: Dark-state of CBD of TtCarH (TR-SFX, SACLA) -

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Basic information

Entry
Database: PDB / ID: 9s06
TitleDark-state of CBD of TtCarH (TR-SFX, SACLA)
ComponentsProbable transcriptional regulator
KeywordsDNA BINDING PROTEIN / SFX / Room temperature / serial crystallography / CarH / photoreceptor / vitamin B12 / cobalamin / coenzyme B12 / time-resolved crystallography
Function / homology
Function and homology information


cobalamin binding / DNA-binding transcription factor activity / DNA binding / metal ion binding / identical protein binding
Similarity search - Function
Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Cobalamin-binding domain superfamily / B12-binding domain profile. ...Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
5'-DEOXYADENOSINE / COBALAMIN / Probable transcriptional regulator
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRios-Santacruz, R. / Coquelle, N. / Colletier, J.P. / De Zitter, E. / Schiro, G. / Weik, M.
Funding support France, 4items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)PhotoGene France
Centre National de la Recherche Scientifique (CNRS)GoToXFEL France
Agence Nationale de la Recherche (ANR)BioXFEL France
Agence Nationale de la Recherche (ANR)SNAPsHOTs France
CitationJournal: Nature / Year: 2026
Title: Integrated structural dynamics uncover new modes of B12 photoreceptor activation
Authors: Rios-Santacruz, R. / Coquelle, N. / Colletier, J.P. / De Zitter, E. / Schiro, G. / Weik, M.
History
DepositionJul 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable transcriptional regulator
B: Probable transcriptional regulator
C: Probable transcriptional regulator
D: Probable transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,36612
Polymers93,0394
Non-polymers6,3268
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19380 Å2
ΔGint-55 kcal/mol
Surface area29690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.800, 71.090, 207.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Probable transcriptional regulator


Mass: 23259.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TT_P0056 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q746J7
#2: Chemical
ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.06 %
Description: plate-like microcrystals with a size around 15umx5umx2um
Crystal growTemperature: 293.15 K / Method: batch mode / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 20% PEG 10000. / Temp details: RT

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Data collection

DiffractionMean temperature: 293.15 K / Ambient temp details: RT / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.55 Å
DetectorType: MPCCD / Detector: CCD / Date: Nov 1, 2022 / Frequency: 30
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 61105 / % possible obs: 100 % / Redundancy: 12903 % / Biso Wilson estimate: 46.1 Å2 / CC1/2: 0.9995 / CC star: 0.9998 / R split: 0.0304 / Net I/σ(I): 22.83
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 9207 % / Mean I/σ(I) obs: 1.87 / Num. unique obs: 4014 / CC1/2: 0.7 / CC star: 0.91 / R split: 0.59 / % possible all: 100
Serial crystallography measurementFocal spot size: 2.24 µm2 / Pulse duration: 10 fsec. / Pulse energy: 300 µJ / Pulse photon energy: 7.996 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: Liquid jet / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: carboxymethyl cellulose / Description: HVE / Injector diameter: 75 µm / Injector nozzle: helium stream / Injector temperature: 293.15 K
Serial crystallography data reductionCrystal hits: 634317 / Frames total: 1709013 / Lattices indexed: 847084

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrystFEL0.10.1data reduction
PHASERphasing
CrystFEL0.10.1data scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→50 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / Phase error: 26.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 3016 4.95 %
Rwork0.1742 --
obs0.1764 60968 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5977 0 436 357 6770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076762
X-RAY DIFFRACTIONf_angle_d0.9919345
X-RAY DIFFRACTIONf_dihedral_angle_d15.7992640
X-RAY DIFFRACTIONf_chiral_restr0.0511019
X-RAY DIFFRACTIONf_plane_restr0.011181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.40241170.42412616X-RAY DIFFRACTION100
2.08-2.120.36941370.3232565X-RAY DIFFRACTION100
2.12-2.150.32631260.27332626X-RAY DIFFRACTION100
2.15-2.190.28421410.25582576X-RAY DIFFRACTION100
2.19-2.230.31751420.25452628X-RAY DIFFRACTION100
2.23-2.280.2921370.2432571X-RAY DIFFRACTION100
2.28-2.330.29791550.22812583X-RAY DIFFRACTION100
2.33-2.380.28991440.2192610X-RAY DIFFRACTION100
2.38-2.440.25111320.20922607X-RAY DIFFRACTION100
2.44-2.510.27261340.20882597X-RAY DIFFRACTION100
2.51-2.580.30711270.21422621X-RAY DIFFRACTION100
2.58-2.670.25751430.21322610X-RAY DIFFRACTION100
2.67-2.760.26361410.21782627X-RAY DIFFRACTION100
2.76-2.870.27861380.22432610X-RAY DIFFRACTION100
2.87-30.25791380.20362654X-RAY DIFFRACTION100
3-3.160.2491380.18792612X-RAY DIFFRACTION100
3.16-3.360.21141230.17162671X-RAY DIFFRACTION100
3.36-3.620.18511410.15852657X-RAY DIFFRACTION100
3.62-3.980.21461430.14632668X-RAY DIFFRACTION100
3.98-4.560.16681510.13192666X-RAY DIFFRACTION100
4.56-5.740.18821430.13972716X-RAY DIFFRACTION100
5.74-40.470.17291250.14742861X-RAY DIFFRACTION99

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