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- PDB-9ff4: The structure of G.kaustophilus T-1 ScoC-17bp dsDNA complex -

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Basic information

Entry
Database: PDB / ID: 9ff4
TitleThe structure of G.kaustophilus T-1 ScoC-17bp dsDNA complex
Components
  • DNA (5'-D(*AP*GP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*TP*TP*TP*AP*T)-3')
  • DNA (5'-D(*TP*AP*AP*TP*AP*AP*AP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*C)-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: 2.8 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-17bp 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
B: HTH-type transcriptional regulator Hpr
C: HTH-type transcriptional regulator Hpr
A: HTH-type transcriptional regulator Hpr
D: HTH-type transcriptional regulator Hpr
H: DNA (5'-D(*TP*AP*AP*TP*AP*AP*AP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*C)-3')
L: DNA (5'-D(*AP*GP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*TP*TP*TP*AP*T)-3')
M: DNA (5'-D(*TP*AP*AP*TP*AP*AP*AP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*C)-3')
F: DNA (5'-D(*AP*GP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*TP*TP*TP*AP*T)-3')
G: DNA (5'-D(*TP*AP*AP*TP*AP*AP*AP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*C)-3')
J: DNA (5'-D(*AP*GP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*TP*TP*TP*AP*T)-3')
K: DNA (5'-D(*TP*AP*AP*TP*AP*AP*AP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*C)-3')
N: DNA (5'-D(*AP*GP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*TP*TP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,61618
Polymers142,43812
Non-polymers1,1786
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34450 Å2
ΔGint-239 kcal/mol
Surface area49390 Å2
Unit cell
Length a, b, c (Å)68.634, 70.546, 95.468
Angle α, β, γ (deg.)89.773, 81.625, 60.911
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 4 molecules BCAD

#1: 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

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DNA chain , 2 types, 8 molecules HMGKLFJN

#2: DNA chain
DNA (5'-D(*TP*AP*AP*TP*AP*AP*AP*AP*TP*AP*AP*AP*AP*AP*AP*AP*TP*C)-3')


Mass: 5532.684 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Geobacillus kaustophilus (bacteria)
#3: DNA chain
DNA (5'-D(*AP*GP*AP*TP*TP*TP*TP*TP*TP*TP*AP*TP*TP*TP*TP*AP*T)-3')


Mass: 5491.582 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Geobacillus kaustophilus (bacteria)

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Non-polymers , 3 types, 55 molecules

#4: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.82 Å3/Da / Density % sol: 56.4 % / Description: Needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 3350 and 0.3 M Magnesium formate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→48.48 Å / Num. obs: 37515 / % possible obs: 98.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 63.56 Å2 / CC1/2: 0.93 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.05 / Rrim(I) all: 0.09 / Net I/σ(I): 6.3
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4515 / CC1/2: 0.51 / Rpim(I) all: 0.39 / Rrim(I) all: 0.77

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.48 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.7648
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2931 1803 4.84 %
Rwork0.2282 35481 -
obs0.2312 37284 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.89 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5936 2848 78 49 8911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119340
X-RAY DIFFRACTIONf_angle_d1.190813128
X-RAY DIFFRACTIONf_chiral_restr0.05831404
X-RAY DIFFRACTIONf_plane_restr0.00681164
X-RAY DIFFRACTIONf_dihedral_angle_d29.90052188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.45151730.38052656X-RAY DIFFRACTION97.65
2.88-2.960.36191710.35962701X-RAY DIFFRACTION98.09
2.96-3.060.36181510.31842722X-RAY DIFFRACTION97.56
3.06-3.170.3731180.2782732X-RAY DIFFRACTION97.84
3.17-3.290.3471190.26372722X-RAY DIFFRACTION97.33
3.29-3.440.35731170.26692723X-RAY DIFFRACTION97.36
3.44-3.620.31991460.25272729X-RAY DIFFRACTION97.92
3.62-3.850.30682100.24142673X-RAY DIFFRACTION98.19
3.85-4.150.27561480.22972744X-RAY DIFFRACTION98.53
4.15-4.560.30331060.20192774X-RAY DIFFRACTION98.87
4.56-5.220.25111090.1982778X-RAY DIFFRACTION98.97
5.22-6.580.28211070.22022771X-RAY DIFFRACTION98.66
6.58-48.480.19841280.1652756X-RAY DIFFRACTION98.4

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