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- PDB-4r24: Complete dissection of B. subtilis nitrogen homeostatic circuitry -

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Basic information

Entry
Database: PDB / ID: 4r24
TitleComplete dissection of B. subtilis nitrogen homeostatic circuitry
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
Keywordstranscrption/DNA / TnrA / GS / B. subtilis / GlnK / New DNA-binding family / with winged HTH / transcription / nucleoid / transcrption-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 / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / 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: 2.25 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 1.1Mar 11, 2015Group: Derived calculations
Revision 1.2Feb 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

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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)16,5252
Polymers16,5252
Non-polymers00
Water1,00956
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)33,0494
Polymers33,0494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6040 Å2
ΔGint-42 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.360, 100.210, 46.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein HTH-type transcriptional regulator TnrA


Mass: 10037.497 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 / Fragment: DNA, 21mer / Source method: obtained synthetically / Details: 21-mer cognate DNA site / Source: (synth.) Synthetic DNA (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG 1500, MES or 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: double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→55 Å / Num. all: 7777 / Num. obs: 7751 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.068 / Net I/σ(I): 26.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.14data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→55 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 846 10.8 %random
Rwork0.2175 ---
obs0.2175 7751 99.1 %-
all-7777 --
Solvent computationBsol: 42.3397 Å2
Displacement parametersBiso max: 86.61 Å2 / Biso mean: 38.7315 Å2 / Biso min: 13.44 Å2
Baniso -1Baniso -2Baniso -3
1--6.796 Å20 Å20 Å2
2--20.091 Å20 Å2
3----13.295 Å2
Refinement stepCycle: LAST / Resolution: 2.25→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms702 431 0 56 1189
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.056
X-RAY DIFFRACTIONc_mcbond_it2.7651.5
X-RAY DIFFRACTIONc_scbond_it4.5082
X-RAY DIFFRACTIONc_mcangle_it3.7222
X-RAY DIFFRACTIONc_scangle_it5.9292.5
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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