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- PDB-8c34: Aerobic light exposed 1.8 Angstrom crystal structure of cobalamin... -

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Basic information

Entry
Database: PDB / ID: 8c34
TitleAerobic light exposed 1.8 Angstrom crystal structure of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH
ComponentsProbable transcriptional regulator
KeywordsTRANSCRIPTION / CarH / cobalamin / light-activated / transcription regulator
Function / homology
Function and homology information


cobalamin binding / DNA-binding transcription factor activity / DNA binding / identical protein binding / metal ion binding
Similarity search - Function
Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / Cobalamin-binding domain superfamily / MerR-type HTH domain / B12-binding domain profile. ...Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / Cobalamin-binding domain superfamily / MerR-type HTH domain / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
COBALAMIN / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Probable transcriptional regulator
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsPoddar, H. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/S030336/1 United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Redox driven B 12 -ligand switch drives CarH photoresponse.
Authors: Poddar, H. / Rios-Santacruz, R. / Heyes, D.J. / Shanmugam, M. / Brookfield, A. / Johannissen, L.O. / Levy, C.W. / Jeffreys, L.N. / Zhang, S. / Sakuma, M. / Colletier, J.P. / Hay, S. / ...Authors: Poddar, H. / Rios-Santacruz, R. / Heyes, D.J. / Shanmugam, M. / Brookfield, A. / Johannissen, L.O. / Levy, C.W. / Jeffreys, L.N. / Zhang, S. / Sakuma, M. / Colletier, J.P. / Hay, S. / Schiro, G. / Weik, M. / Scrutton, N.S. / Leys, D.
History
DepositionDec 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)98,61710
Polymers93,0394
Non-polymers5,5786
Water11,872659
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17150 Å2
ΔGint-57 kcal/mol
Surface area30480 Å2
Unit cell
Length a, b, c (Å)60.870, 72.690, 201.560
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 HB27 (bacteria) / Gene: TT_P0056 / Production host: Escherichia coli (E. coli) / References: UniProt: Q746J7
#2: Chemical
ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 659 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Condition B3 from Morpheus screen (Molecular Dimensions) (0.09 M halogens, 0.1 M buffer system 1 pH 6.5, 30% v/v precipitant mix 3) Cryo-protected crystals exposed to bright 530 nm LED ...Details: Condition B3 from Morpheus screen (Molecular Dimensions) (0.09 M halogens, 0.1 M buffer system 1 pH 6.5, 30% v/v precipitant mix 3) Cryo-protected crystals exposed to bright 530 nm LED (Thorlabs) for 1-5 secs under aerobic conditions

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.82→52.1 Å / Num. obs: 81098 / % possible obs: 100 % / Redundancy: 25.7 % / CC1/2: 1 / Net I/σ(I): 19
Reflection shellResolution: 1.82→1.85 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3892 / CC1/2: 0.5 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMACREFMAC 5.8.0352refinement
xia2.multiplexdata reduction
xia2.multiplexdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8C31

8c31


Resolution: 1.82→52.1 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.198 4035 -
Rwork0.166 --
obs-81010 100 %
Refinement stepCycle: LAST / Resolution: 1.82→52.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6025 0 381 659 7065
LS refinement shellResolution: 1.82→1.87 Å /
Rfactor% reflection
Rfree0.319 -
obs0.293 98.2 %

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