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- PDB-9s0g: Intermediate-state of CBD of TtCarH after illumination at 180 K (... -

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Basic information

Entry
Database: PDB / ID: 9s0g
TitleIntermediate-state of CBD of TtCarH after illumination at 180 K (MX, ESRF)
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 / BROMIDE ION / GLYCINE / Probable transcriptional regulator
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchianchi, S. / Coquelle, N. / Poddar, H. / Rios-Santacruz, R. / Schiro, G. / Weik, M.
Funding support France, United Kingdom, 5items
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
Engineering and Physical Sciences Research CouncilEP/P001548/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/S030336/1 United Kingdom
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)99,78719
Polymers93,0394
Non-polymers6,74815
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20390 Å2
ΔGint-98 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.990, 70.130, 206.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q746J7

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Non-polymers , 6 types, 365 molecules

#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: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Morpheus screen condition B3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→49.1 Å / Num. obs: 73255 / % possible obs: 98.9 % / Redundancy: 11.1 % / CC1/2: 0.999 / CC star: 0.999 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→1.95 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 5391 / CC1/2: 0.467 / CC star: 0.798 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→41.55 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / Phase error: 28.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 3660 5 %
Rwork0.2049 --
obs0.2066 73218 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5803 0 447 350 6600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076514
X-RAY DIFFRACTIONf_angle_d1.029013
X-RAY DIFFRACTIONf_dihedral_angle_d14.9152478
X-RAY DIFFRACTIONf_chiral_restr0.0571001
X-RAY DIFFRACTIONf_plane_restr0.011138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.4031380.36352628X-RAY DIFFRACTION100
1.93-1.950.36541380.35912627X-RAY DIFFRACTION97
1.95-1.980.39591400.35072647X-RAY DIFFRACTION100
1.98-2.010.34991370.3052610X-RAY DIFFRACTION98
2.01-2.040.35211350.2962561X-RAY DIFFRACTION97
2.04-2.070.32351400.26912660X-RAY DIFFRACTION98
2.07-2.110.3261400.25282657X-RAY DIFFRACTION100
2.11-2.150.31241380.24772625X-RAY DIFFRACTION98
2.15-2.190.30321390.25582639X-RAY DIFFRACTION99
2.19-2.230.3331400.24842651X-RAY DIFFRACTION99
2.23-2.280.2741400.24392670X-RAY DIFFRACTION99
2.28-2.340.29741410.22812665X-RAY DIFFRACTION99
2.34-2.390.30421410.23192683X-RAY DIFFRACTION100
2.39-2.460.29281360.23112590X-RAY DIFFRACTION97
2.46-2.530.30511400.24372649X-RAY DIFFRACTION99
2.53-2.610.30471410.22922682X-RAY DIFFRACTION99
2.61-2.710.27441420.21892706X-RAY DIFFRACTION100
2.71-2.810.27471410.22272676X-RAY DIFFRACTION100
2.81-2.940.23791420.22842696X-RAY DIFFRACTION100
2.94-3.10.29141420.23722703X-RAY DIFFRACTION100
3.1-3.290.27261400.21642652X-RAY DIFFRACTION97
3.29-3.550.26221440.20692738X-RAY DIFFRACTION100
3.55-3.90.22561440.19082737X-RAY DIFFRACTION100
3.9-4.470.17711450.15762751X-RAY DIFFRACTION100
4.47-5.620.17651450.16292762X-RAY DIFFRACTION98
5.62-41.550.17171510.17062893X-RAY DIFFRACTION98

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