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- PDB-9s09: 300 ns Intermediate-state of CBD of TtCarH at 30 mJ/cm2 laser flu... -

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Basic information

Entry
Database: PDB / ID: 9s09
Title300 ns Intermediate-state of CBD of TtCarH at 30 mJ/cm2 laser fluence (TR-SFX, SACLA), refined against extrapolated structure factors
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: 2.3 Å
AuthorsRios-Santacruz, R. / Coquelle, N. / Colletier, J.P. / De Zitter, E. / Schiro, G. / Weik, M.
Funding support France, 3items
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
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
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18640 Å2
ΔGint-64 kcal/mol
Surface area30040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.800, 71.080, 207.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: obtained synthetically / 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.: 209 / 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: 52.05 %
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.

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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: 2.3→50 Å / Num. obs: 43554 / % possible obs: 100 % / Redundancy: 1374 % / CC1/2: 0.996 / CC star: 0.999 / R split: 0.0829 / Net I/σ(I): 9.4
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 977 % / Mean I/σ(I) obs: 1.03 / Num. unique obs: 2846 / CC1/2: 0.546 / CC star: 0.837 / R split: 1.05 / % 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: 63544 / Frames total: 241824 / Lattices indexed: 83486

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrystFEL0.10.1data reduction
CrystFEL0.10.1data scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.31 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / Phase error: 42.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3284 1995 4.6 %
Rwork0.2768 --
obs0.2792 43364 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5948 0 436 209 6593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066653
X-RAY DIFFRACTIONf_angle_d0.9679182
X-RAY DIFFRACTIONf_dihedral_angle_d15.632585
X-RAY DIFFRACTIONf_chiral_restr0.0491000
X-RAY DIFFRACTIONf_plane_restr0.0081160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.45741380.43892894X-RAY DIFFRACTION100
2.36-2.420.47381410.4142905X-RAY DIFFRACTION100
2.42-2.490.42681410.42682920X-RAY DIFFRACTION100
2.49-2.570.45581400.42642898X-RAY DIFFRACTION100
2.57-2.660.48531410.41632913X-RAY DIFFRACTION100
2.66-2.770.46891400.38932927X-RAY DIFFRACTION100
2.77-2.90.431430.38352950X-RAY DIFFRACTION100
2.9-3.050.45251400.35552924X-RAY DIFFRACTION100
3.05-3.240.39541440.32742970X-RAY DIFFRACTION100
3.24-3.490.35881410.29562932X-RAY DIFFRACTION100
3.49-3.840.31091440.26682970X-RAY DIFFRACTION100
3.84-4.40.25991430.22262992X-RAY DIFFRACTION100
4.4-5.530.26851460.21143015X-RAY DIFFRACTION100
5.53-29.310.23591530.19193159X-RAY DIFFRACTION100

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