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- PDB-9s07: 3 us Intermediate-state of CBD of TtCarH at 30 mJ/cm2 laser fluen... -

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Basic information

Entry
Database: PDB / ID: 9s07
Title3 us Intermediate-state of CBD of TtCarH at 30 mJ/cm2 laser fluence (TR-SFX, SwissFEL), 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: 2.6 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
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18860 Å2
ΔGint-59 kcal/mol
Surface area31110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.520, 72.130, 209.530
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.: 134 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
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 / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESC / Wavelength: 1.13 Å
DetectorType: PSI JUNGFRAU 8M / Detector: PIXEL / Date: Jun 7, 2024 / Frequency: 100
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 31460 / % possible obs: 100 % / Redundancy: 501 % / Biso Wilson estimate: 51.64 Å2 / CC1/2: 0.986 / CC star: 0.997 / R split: 0.136 / Net I/σ(I): 5.9
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 349 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2056 / CC1/2: 0.541 / CC star: 0.838 / R split: 1.034 / % possible all: 100
Serial crystallography measurementFocal spot size: 15.54 µm2 / Pulse duration: 35 fsec. / Pulse energy: 280 µJ / Pulse photon energy: 11 keV / XFEL pulse repetition rate: 100 Hz
Serial crystallography sample deliveryDescription: Fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: micro-structured polymer fixed targets / Sample dehydration prevention: mylar film / Sample holding: mesh
Serial crystallography data reductionCrystal hits: 44725 / Frames total: 65740 / Lattices indexed: 33798

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrystFEL0.10.1data scaling
CrystFEL0.10.1data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.96 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / Phase error: 39.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3254 1561 5 %
Rwork0.2642 --
obs0.2673 31251 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5923 0 436 134 6493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096645
X-RAY DIFFRACTIONf_angle_d1.2049174
X-RAY DIFFRACTIONf_dihedral_angle_d18.3392589
X-RAY DIFFRACTIONf_chiral_restr0.0541005
X-RAY DIFFRACTIONf_plane_restr0.011156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.46481380.42462633X-RAY DIFFRACTION99
2.68-2.780.4261410.42112659X-RAY DIFFRACTION100
2.78-2.890.47151400.3952655X-RAY DIFFRACTION100
2.89-3.020.39971380.3722656X-RAY DIFFRACTION100
3.02-3.180.43251400.37792673X-RAY DIFFRACTION100
3.18-3.380.39981410.33332665X-RAY DIFFRACTION100
3.38-3.640.38431420.29842703X-RAY DIFFRACTION100
3.64-40.35721420.26022693X-RAY DIFFRACTION100
4-4.570.29741430.21232716X-RAY DIFFRACTION100
4.57-5.740.26131460.21422762X-RAY DIFFRACTION100
5.74-19.960.23471500.19532875X-RAY DIFFRACTION100

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