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- PDB-9s0h: Dark-state of CBD of TtCarH mutant - H132A (SSX, DLS) -

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Basic information

Entry
Database: PDB / ID: 9s0h
TitleDark-state of CBD of TtCarH mutant - H132A (SSX, DLS)
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPoddar, H. / Coquelle, N. / Axford, D. / Rios-Santacruz, R. / Leys, D. / Owen, R.L.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
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)99,09712
Polymers92,7714
Non-polymers6,3268
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19300 Å2
ΔGint-62 kcal/mol
Surface area29290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.497, 71.468, 206.502
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: 23192.730 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-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: rod-shaped crystals of around 15umx8umx 5um
Crystal growTemperature: 293.15 K / Method: batch mode / pH: 5.8
Details: 0.1 M ammonium sulfate, 0.1 M sodium citrate, pH 5.8, 16% w/v PEG 4000, 20% v/v glycerol
Temp details: RT

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Data collection

DiffractionMean temperature: 293.15 K / Ambient temp details: RT / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→103.19 Å / Num. obs: 65184 / % possible obs: 100 % / Redundancy: 52.6 % / Biso Wilson estimate: 27.49 Å2 / CC1/2: 0.991 / R split: 0.125 / Net I/σ(I): 7
Reflection shellResolution: 2→2.03 Å / Redundancy: 41.25 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3195 / CC1/2: 0.408 / R split: 0.905 / % possible all: 100
Serial crystallography sample deliveryDescription: Fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: silicon chip / Sample dehydration prevention: mylar film / Sample holding: mesh

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACTdata extraction
xia23.22.1data reduction
xia23.22.1data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→54.7 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 3218 4.96 %
Rwork0.2003 --
obs0.2023 64882 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→54.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5921 0 436 328 6685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076604
X-RAY DIFFRACTIONf_angle_d1.079116
X-RAY DIFFRACTIONf_dihedral_angle_d15.0132553
X-RAY DIFFRACTIONf_chiral_restr0.054995
X-RAY DIFFRACTIONf_plane_restr0.011140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.36371450.34172270X-RAY DIFFRACTION87
2.03-2.060.35231230.32052590X-RAY DIFFRACTION96
2.06-2.10.34911260.30212637X-RAY DIFFRACTION98
2.1-2.130.35661370.28952619X-RAY DIFFRACTION99
2.13-2.170.29141560.2762658X-RAY DIFFRACTION100
2.17-2.210.3341300.26622661X-RAY DIFFRACTION100
2.21-2.260.29781520.25362649X-RAY DIFFRACTION100
2.26-2.310.29511310.23952724X-RAY DIFFRACTION100
2.31-2.360.2521400.23042646X-RAY DIFFRACTION100
2.36-2.420.27561260.22542684X-RAY DIFFRACTION100
2.42-2.480.25761450.21862720X-RAY DIFFRACTION100
2.48-2.560.22281310.22492665X-RAY DIFFRACTION100
2.56-2.640.29111570.20972671X-RAY DIFFRACTION100
2.64-2.730.26421390.20682690X-RAY DIFFRACTION100
2.73-2.840.27241390.20072706X-RAY DIFFRACTION100
2.84-2.970.23831220.20382705X-RAY DIFFRACTION100
2.97-3.130.2651470.2082716X-RAY DIFFRACTION100
3.13-3.330.23171300.19062724X-RAY DIFFRACTION100
3.33-3.580.23391330.17982759X-RAY DIFFRACTION100
3.58-3.940.23061460.16982702X-RAY DIFFRACTION100
3.94-4.510.1871670.15542734X-RAY DIFFRACTION100
4.51-5.690.18391320.17052813X-RAY DIFFRACTION100
5.69-54.70.18881640.15722921X-RAY DIFFRACTION100

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