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- PDB-6c31: Crystal structure of TetR family protein Rv0078 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 6c31
TitleCrystal structure of TetR family protein Rv0078 in complex with DNA
Components
  • DNA (5'-D(*GP*TP*TP*AP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*GP*CP*TP*TP*GP*TP*AP*AP*A)-3')
  • DNA (5'-D(P*AP*CP*AP*AP*GP*CP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*TP*AP*AP*C)-3')
  • TetR family transcriptional regulator
KeywordsDNA BINDING PROTEIN/DNA / Rv0078 / DNA / TetR family / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / plasma membrane
Similarity search - Function
: / Tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Probable transcriptional regulatory protein / Probable transcriptional regulatory protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Mycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHsu, H.C. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI070285 United States
CitationJournal: MBio / Year: 2018
Title: Cytokinin Signaling in Mycobacterium tuberculosis.
Authors: Samanovic, M.I. / Hsu, H.C. / Jones, M.B. / Jones, V. / McNeil, M.R. / Becker, S.H. / Jordan, A.T. / Strnad, M. / Xu, C. / Jackson, M. / Li, H. / Darwin, K.H.
History
DepositionJan 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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: TetR family transcriptional regulator
B: TetR family transcriptional regulator
C: TetR family transcriptional regulator
D: TetR family transcriptional regulator
E: TetR family transcriptional regulator
F: TetR family transcriptional regulator
G: TetR family transcriptional regulator
H: TetR family transcriptional regulator
I: DNA (5'-D(P*AP*CP*AP*AP*GP*CP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*TP*AP*AP*C)-3')
J: DNA (5'-D(*GP*TP*TP*AP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*GP*CP*TP*TP*GP*TP*AP*AP*A)-3')
K: DNA (5'-D(P*AP*CP*AP*AP*GP*CP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*TP*AP*AP*C)-3')
L: DNA (5'-D(*GP*TP*TP*AP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*GP*CP*TP*TP*GP*TP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)216,06612
Polymers216,06612
Non-polymers00
Water0
1
A: TetR family transcriptional regulator
B: TetR family transcriptional regulator
C: TetR family transcriptional regulator
D: TetR family transcriptional regulator
K: DNA (5'-D(P*AP*CP*AP*AP*GP*CP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*TP*AP*AP*C)-3')
L: DNA (5'-D(*GP*TP*TP*AP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*GP*CP*TP*TP*GP*TP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)108,0336
Polymers108,0336
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-110 kcal/mol
Surface area38470 Å2
MethodPISA
2
E: TetR family transcriptional regulator
F: TetR family transcriptional regulator
G: TetR family transcriptional regulator
H: TetR family transcriptional regulator
I: DNA (5'-D(P*AP*CP*AP*AP*GP*CP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*TP*AP*AP*C)-3')
J: DNA (5'-D(*GP*TP*TP*AP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*GP*CP*TP*TP*GP*TP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)108,0336
Polymers108,0336
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13830 Å2
ΔGint-111 kcal/mol
Surface area38720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.039, 80.040, 186.660
Angle α, β, γ (deg.)90.000, 90.070, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
TetR family transcriptional regulator / Rv0078


Mass: 23477.922 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: LH57_00450 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L0T5M0, UniProt: O53623*PLUS
#2: DNA chain DNA (5'-D(P*AP*CP*AP*AP*GP*CP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*TP*AP*AP*C)-3')


Mass: 7049.574 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)
#3: DNA chain DNA (5'-D(*GP*TP*TP*AP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*GP*CP*TP*TP*GP*TP*AP*AP*A)-3')


Mass: 7071.570 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)

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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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium formate dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 3→28.74 Å / Num. obs: 46330 / % possible obs: 94.8 % / Redundancy: 6.4 % / Rpim(I) all: 0.087 / Net I/σ(I): 5.5
Reflection shellResolution: 3→3.16 Å / Rpim(I) all: 0.474

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5WM9

5wm9


Resolution: 3→28.495 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 4556 9.89 %random
Rwork0.2019 ---
obs0.2065 46083 94.42 %-
Displacement parametersBiso mean: 73 Å2
Refinement stepCycle: LAST / Resolution: 3→28.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11879 1760 0 0 13639

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