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- PDB-5c8f: Crystal structure of light-exposed full-length Thermus thermophil... -

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Basic information

Entry
Database: PDB / ID: 5c8f
TitleCrystal structure of light-exposed full-length Thermus thermophilus CarH bound to cobalamin
ComponentsLight-dependent transcriptional regulator CarH
KeywordsTRANSCRIPTIONAL REGULATOR / Transcription factor / light sensor / adenosylcobalamin-binding / DNA-binding / TRANSCRIPTION
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 / Probable transcriptional regulator
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsJost, M. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069857 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2015
Title: Structural basis for gene regulation by a B12-dependent photoreceptor.
Authors: Jost, M. / Fernandez-Zapata, J. / Polanco, M.C. / Ortiz-Guerrero, J.M. / Chen, P.Y. / Kang, G. / Padmanabhan, S. / Elias-Arnanz, M. / Drennan, C.L.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Light-dependent transcriptional regulator CarH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8175
Polymers33,3231
Non-polymers1,4934
Water34219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Light-dependent transcriptional regulator CarH
hetero molecules

A: Light-dependent transcriptional regulator CarH
hetero molecules

A: Light-dependent transcriptional regulator CarH
hetero molecules

A: Light-dependent transcriptional regulator CarH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,26620
Polymers133,2934
Non-polymers5,97316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-11
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_554y,x,-z-11
Buried area15970 Å2
ΔGint-129 kcal/mol
Surface area41670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.910, 126.910, 149.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsMonomer assembly has been verified by size exclusion chromatography and analytical ultracentrifugation. Importantly, only this particular form of the CarH protein (light-exposed CarH) is monomeric.

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Components

#1: Protein Light-dependent transcriptional regulator CarH


Mass: 33323.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_P0056 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star pLysS / References: UniProt: Q746J7
#2: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.52 Å3/Da / Density % sol: 72.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 3.4 M NaCl, 0.1 M Bis-Tris pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 23, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.65→100 Å / Num. obs: 18067 / % possible obs: 100 % / Redundancy: 12.8 % / Rsym value: 0.069 / Net I/σ(I): 26.8
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JML

2jml


Resolution: 2.65→89.74 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.203 896 4.96 %Random selection
Rwork0.172 ---
obs0.174 18061 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→89.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 99 19 2208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052248
X-RAY DIFFRACTIONf_angle_d0.7293071
X-RAY DIFFRACTIONf_dihedral_angle_d10.559872
X-RAY DIFFRACTIONf_chiral_restr0.03335
X-RAY DIFFRACTIONf_plane_restr0.004421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6502-2.81620.34741450.30262809X-RAY DIFFRACTION100
2.8162-3.03370.321520.25282795X-RAY DIFFRACTION100
3.0337-3.3390.26461620.21292825X-RAY DIFFRACTION100
3.339-3.82210.20381390.17122853X-RAY DIFFRACTION100
3.8221-4.81540.16821580.14332859X-RAY DIFFRACTION100
4.8154-89.79040.17991400.15853024X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.786 Å / Origin y: 4.4298 Å / Origin z: -52.9519 Å
111213212223313233
T0.7864 Å2-0.1881 Å2-0.0764 Å2-0.5907 Å2-0.0284 Å2--0.5711 Å2
L1.5618 °2-0.7518 °20.3808 °2-3.3027 °2-0.709 °2--1.8068 °2
S-0.1032 Å °-0.2439 Å °0.1441 Å °0.8324 Å °-0.1536 Å °-0.3836 Å °-0.2414 Å °0.1617 Å °0.2719 Å °
Refinement TLS groupSelection details: (chain 'A' )

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