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- PDB-4r22: TnrA-DNA complex -

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Basic information

Entry
Database: PDB / ID: 4r22
TitleTnrA-DNA complex
Components
  • DNA (5'-D(*CP*GP*TP*GP*TP*AP*AP*GP*GP*AP*AP*TP*TP*CP*TP*GP*AP*CP*AP*CP*G)-3')
  • HTH-type transcriptional regulator TnrA
Keywordstranscription/DNA / New family of transcription regulators / Transcription / GS / transcription-DNA complex
Function / homology
Function and homology information


nitrogen catabolite activation of transcription / cellular response to nitrogen levels / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / HTH-type transcriptional regulator TnrA
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
Synthetic DNA (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSchumacher, M.A.
CitationJournal: Genes Dev. / Year: 2015
Title: Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis.
Authors: Schumacher, M.A. / Chinnam, N.B. / Cuthbert, B. / Tonthat, N.K. / Whitfill, T.
History
DepositionAug 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: HTH-type transcriptional regulator TnrA
G: DNA (5'-D(*CP*GP*TP*GP*TP*AP*AP*GP*GP*AP*AP*TP*TP*CP*TP*GP*AP*CP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)16,1952
Polymers16,1952
Non-polymers00
Water00
1
B: HTH-type transcriptional regulator TnrA
G: DNA (5'-D(*CP*GP*TP*GP*TP*AP*AP*GP*GP*AP*AP*TP*TP*CP*TP*GP*AP*CP*AP*CP*G)-3')

B: HTH-type transcriptional regulator TnrA
G: DNA (5'-D(*CP*GP*TP*GP*TP*AP*AP*GP*GP*AP*AP*TP*TP*CP*TP*GP*AP*CP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)32,3914
Polymers32,3914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6010 Å2
ΔGint-39 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.440, 46.390, 42.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HTH-type transcriptional regulator TnrA


Mass: 9708.124 Da / Num. of mol.: 1 / Fragment: TnrA / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: WSH-002 / Gene: tnrA, BMWSH_3277 / Production host: Escherichia coli (E. coli) / References: UniProt: G2RUZ1
#2: DNA chain DNA (5'-D(*CP*GP*TP*GP*TP*AP*AP*GP*GP*AP*AP*TP*TP*CP*TP*GP*AP*CP*AP*CP*G)-3')


Mass: 6487.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 21-mer cognate DNA site / Source: (synth.) Synthetic DNA (others)

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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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 1500, 0.1M MMT buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2013
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→54.6 Å / Num. all: 3799 / Num. obs: 3759 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06 / Rsym value: 0.07 / Net I/σ(I): 22.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
PHASERphasing
CNSrefinement
PDB_EXTRACT3.14data extraction
ADSCQuantumdata collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→54.6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2787 722 16.6 %random
Rwork0.2606 ---
all0.2606 3799 --
obs0.2606 3759 86.4 %-
Solvent computationBsol: 62.9258 Å2
Displacement parametersBiso max: 118.8 Å2 / Biso mean: 59.3982 Å2 / Biso min: 23.06 Å2
Baniso -1Baniso -2Baniso -3
1-1.124 Å20 Å20 Å2
2---15.77 Å20 Å2
3---14.646 Å2
Refinement stepCycle: LAST / Resolution: 2.6→54.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms679 431 0 0 1110
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_d2.179
X-RAY DIFFRACTIONc_mcbond_it4.5681.5
X-RAY DIFFRACTIONc_scbond_it5.5692
X-RAY DIFFRACTIONc_mcangle_it6.1032
X-RAY DIFFRACTIONc_scangle_it6.3852.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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