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- PDB-9ff5: The structure of G.kaustophilus T-1 ScoC-23bp dsDNA complex -

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Basic information

Entry
Database: PDB / ID: 9ff5
TitleThe structure of G.kaustophilus T-1 ScoC-23bp dsDNA complex
Components
  • DNA (5'-D(*AP*AP*TP*AP*TP*AP*TP*T)-3')
  • DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*TP*TP*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*TP*AP*TP*T)-3')
  • DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*TP*TP*TP*TP*GP*TP*TP*AP*AP*TP*AP*AP*TP*AP*TP*T)-3')
  • HTH-type transcriptional regulator Hpr
KeywordsDNA BINDING PROTEIN / ScoC / Global regulator / Geobacillus kaustophilus / Tetramer / DNA bending / Hpr
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / response to stress / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
HTH-type transcriptional regulator Hpr / Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / HTH-type transcriptional regulator Hpr
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHadad, N. / Shulami, S. / Pomyalov, S. / Shoham, Y. / Shoham, G.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation500/10 Israel
CitationJournal: To be Published
Title: The structure of G.kaustophilus T-1 ScoC-23bp dsDNA complex
Authors: Hadad, N. / Shulami, S. / Pomyalov, S. / Shoham, Y. / Shoham, G.
History
DepositionMay 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*TP*TP*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*TP*AP*TP*T)-3')
J: DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*TP*TP*TP*TP*GP*TP*TP*AP*AP*TP*AP*AP*TP*AP*TP*T)-3')
B: HTH-type transcriptional regulator Hpr
C: HTH-type transcriptional regulator Hpr
A: HTH-type transcriptional regulator Hpr
D: HTH-type transcriptional regulator Hpr
E: DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*TP*TP*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*TP*AP*TP*T)-3')
G: DNA (5'-D(*AP*AP*TP*AP*TP*AP*TP*T)-3')
F: DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*TP*TP*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*TP*AP*TP*T)-3')
H: DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*TP*TP*TP*TP*GP*TP*TP*AP*AP*TP*AP*AP*TP*AP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)136,04210
Polymers136,04210
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28410 Å2
ΔGint-206 kcal/mol
Surface area51990 Å2
Unit cell
Length a, b, c (Å)88.205, 100.147, 96.606
Angle α, β, γ (deg.)90.000, 112.335, 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: DNA chain DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*TP*TP*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*TP*AP*TP*T)-3')


Mass: 7053.649 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Geobacillus kaustophilus (bacteria)
#2: DNA chain DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*TP*TP*TP*TP*GP*TP*TP*AP*AP*TP*AP*AP*TP*AP*TP*T)-3')


Mass: 7057.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Geobacillus kaustophilus (bacteria)
#3: Protein
HTH-type transcriptional regulator Hpr / Protease production regulatory protein Hpr


Mass: 24585.248 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: hpr, GK0652 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5L293
#4: DNA chain DNA (5'-D(*AP*AP*TP*AP*TP*AP*TP*T)-3')


Mass: 2424.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geobacillus kaustophilus (bacteria)
Has protein modificationN

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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: 2.91 Å3/Da / Density % sol: 57.79 % / Description: Needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 40% MPD and 0.08M Magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 3.5→42.68 Å / Num. obs: 21515 / % possible obs: 98.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 115.21 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.098 / Rrim(I) all: 0.164 / Net I/σ(I): 6.6
Reflection shellResolution: 3.5→3.62 Å / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4173 / CC1/2: 0.54 / Rpim(I) all: 0.62 / Rrim(I) all: 1.06

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→42.68 Å / SU ML: 0.591 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.1226
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2824 891 4.53 %
Rwork0.2331 18790 -
obs0.2353 19681 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 108 Å2
Refinement stepCycle: LAST / Resolution: 3.5→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5936 2464 0 0 8400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138836
X-RAY DIFFRACTIONf_angle_d1.386612392
X-RAY DIFFRACTIONf_chiral_restr0.07191330
X-RAY DIFFRACTIONf_plane_restr0.00861145
X-RAY DIFFRACTIONf_dihedral_angle_d27.2061936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.720.37691460.31133088X-RAY DIFFRACTION98.75
3.72-4.010.33281250.26563161X-RAY DIFFRACTION99.88
4.01-4.410.271550.22183110X-RAY DIFFRACTION99.85
4.41-5.050.25281510.2013115X-RAY DIFFRACTION99.88
5.05-6.350.29441660.24443152X-RAY DIFFRACTION99.94
6.36-42.680.2621480.2223164X-RAY DIFFRACTION98.81

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