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- PDB-7bca: Crystal structure of the HTH DNA binding protein ArdK from R388 p... -

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Basic information

Entry
Database: PDB / ID: 7bca
TitleCrystal structure of the HTH DNA binding protein ArdK from R388 plasmid bound to a direct-repeat DNA element
Components
  • DNA (5'-D(*GP*TP*AP*TP*TP*GP*AP*CP*AP*CP*CP*TP*AP*TP*TP*GP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*AP*AP*TP*AP*GP*GP*TP*GP*TP*CP*AP*AP*TP*AP*C)-3')
  • KORA domain-containing protein
KeywordsDNA BINDING PROTEIN / Helix Turn Helix / Direct repeat / Plasmid conjugation
Function / homologyTrfB transcriptional repressor protein / TrfB plasmid transcriptional repressor / RNA polymerase sigma factor, region 3/4-like / DNA / DNA (> 10) / TrfB transcriptional repressor protein domain-containing protein
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsFernandez-Lopez, R. / Boer, D.R. / Moncalian, G.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-55534-C2-2-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-093885-B-I00 Spain
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors.
Authors: Fernandez-Lopez, R. / Ruiz, R. / Del Campo, I. / Gonzalez-Montes, L. / Boer, D.R. / de la Cruz, F. / Moncalian, G.
History
DepositionDec 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KORA domain-containing protein
B: KORA domain-containing protein
C: DNA (5'-D(*TP*GP*TP*CP*AP*AP*TP*AP*GP*GP*TP*GP*TP*CP*AP*AP*TP*AP*C)-3')
D: DNA (5'-D(*GP*TP*AP*TP*TP*GP*AP*CP*AP*CP*CP*TP*AP*TP*TP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)34,0644
Polymers34,0644
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-54 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.120, 39.060, 120.040
Angle α, β, γ (deg.)90.000, 101.650, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein KORA domain-containing protein


Mass: 11208.374 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: R388 plasmid / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Plasmid: pET29c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6I6B7
#2: DNA chain DNA (5'-D(*TP*GP*TP*CP*AP*AP*TP*AP*GP*GP*TP*GP*TP*CP*AP*AP*TP*AP*C)-3')


Mass: 5843.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: R388 plasmid / Source: (synth.) Escherichia coli K-12 (bacteria)
#3: DNA chain DNA (5'-D(*GP*TP*AP*TP*TP*GP*AP*CP*AP*CP*CP*TP*AP*TP*TP*GP*AP*CP*A)-3')


Mass: 5803.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: R388 Plasmid / Source: (synth.) Escherichia coli K-12 (bacteria)
Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 4,000, 10% 2-propanol, 0.1 M Tris-HCl [pH 7.5]

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→58.78 Å / Num. obs: 10025 / % possible obs: 98.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 77.27 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.071 / Net I/σ(I): 10.4
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1437 / CC1/2: 0.901 / Rrim(I) all: 0.462

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
MOSFLM7.2.2data reduction
SCALACCP4 7.0.078data scaling
PHENIX1.17.1_3660phasing
Coot0.0.2model building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.8→58.78 Å / SU ML: 0.4476 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.5429
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2926 491 4.97 %RANDOM
Rwork0.2316 9380 --
obs0.2345 9871 97.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.4 Å2
Refinement stepCycle: LAST / Resolution: 2.8→58.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 773 0 0 2268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392376
X-RAY DIFFRACTIONf_angle_d0.71953369
X-RAY DIFFRACTIONf_chiral_restr0.0364382
X-RAY DIFFRACTIONf_plane_restr0.006309
X-RAY DIFFRACTIONf_dihedral_angle_d23.4109582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.080.40551370.34282314X-RAY DIFFRACTION99.15
3.08-3.530.34791170.2942298X-RAY DIFFRACTION95.27
3.53-4.440.27561130.21862404X-RAY DIFFRACTION99.37
4.44-58.780.25731240.2012364X-RAY DIFFRACTION94.96

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