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- PDB-8qa9: Crystal structure of the RK2 plasmid encoded co-complex of the C-... -

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Basic information

Entry
Database: PDB / ID: 8qa9
TitleCrystal structure of the RK2 plasmid encoded co-complex of the C-terminally truncated transcriptional repressor protein KorB complexed with the partner repressor protein KorA bound to OA-DNA
Components
  • DNA (5'-D(*TP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*A)-3')
  • Transcriptional repressor protein KorB
  • TrfB transcriptional repressor protein
KeywordsDNA BINDING PROTEIN / multi-drug resistance / ParABS / clamp / CTP switch / DNA segregation / gene expression regulation
Function / homology
Function and homology information


chromosome segregation / chromosome / negative regulation of DNA-templated transcription / protein-containing complex / DNA binding / identical protein binding
Similarity search - Function
KorB, C-terminal / Repressor KorB domain / KorB, C-terminal domain superfamily / KorB DNA-binding domain / KorB C-terminal beta-barrel domain / KorB domain / TrfB transcriptional repressor protein / TrfB plasmid transcriptional repressor / : / : ...KorB, C-terminal / Repressor KorB domain / KorB, C-terminal domain superfamily / KorB DNA-binding domain / KorB C-terminal beta-barrel domain / KorB domain / TrfB transcriptional repressor protein / TrfB plasmid transcriptional repressor / : / : / ParB/RepB/Spo0J partition protein / ParB N-terminal domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / Transcriptional repressor, C-terminal
Similarity search - Domain/homology
DNA / DNA (> 10) / TrfB transcriptional repressor protein / Transcriptional repressor protein KorB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMcLean, T.C. / Mundy, J.E.A. / Lawson, D.M. / Le, T.B.K.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01097X/1 United Kingdom
Wellcome Trust221776/Z/20/Z United Kingdom
Royal SocietyURF/R/201020 United Kingdom
CitationJournal: Nat Microbiol / Year: 2025
Title: KorB switching from DNA-sliding clamp to repressor mediates long-range gene silencing in a multi-drug resistance plasmid.
Authors: McLean, T.C. / Balaguer-Perez, F. / Chandanani, J. / Thomas, C.M. / Aicart-Ramos, C. / Burick, S. / Olinares, P.D.B. / Gobbato, G. / Mundy, J.E.A. / Chait, B.T. / Lawson, D.M. / Darst, S.A. ...Authors: McLean, T.C. / Balaguer-Perez, F. / Chandanani, J. / Thomas, C.M. / Aicart-Ramos, C. / Burick, S. / Olinares, P.D.B. / Gobbato, G. / Mundy, J.E.A. / Chait, B.T. / Lawson, D.M. / Darst, S.A. / Campbell, E.A. / Moreno-Herrero, F. / Le, T.B.K.
History
DepositionAug 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional repressor protein KorB
B: Transcriptional repressor protein KorB
C: TrfB transcriptional repressor protein
D: TrfB transcriptional repressor protein
E: DNA (5'-D(*TP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*A)-3')
F: DNA (5'-D(*TP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,57611
Polymers87,0966
Non-polymers4805
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11640 Å2
ΔGint-136 kcal/mol
Surface area35830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.253, 77.095, 84.609
Angle α, β, γ (deg.)90.00, 107.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcriptional repressor protein KorB


Mass: 26418.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The crystallised sequence corresponds to residues 30-253 of the full 358-residue wild-type sequence appended with a C-terminal hexa-histidine tag via a short linker sequence KLAAALE.
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: korB / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07674
#2: Protein TrfB transcriptional repressor protein


Mass: 12850.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The crystallised sequence corresponds to the full-length 101-residue wild-type KorA protein appended with a C-terminal hexa-histidine tag via a short linker sequence KLAAALE.
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trfB / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03052
#3: DNA chain DNA (5'-D(*TP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*A)-3')


Mass: 4278.815 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic short double-stranded DNA sequence containing the KorA binding motif OA
Source: (synth.) Escherichia coli (E. coli)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.12 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→82.65 Å / Num. obs: 29438 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 58.1 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.039 / Rrim(I) all: 0.135 / Χ2: 0.59 / Net I/σ(I): 14.1
Reflection shellResolution: 2.7→2.83 Å / % possible obs: 100 % / Redundancy: 11.6 % / Rmerge(I) obs: 1.533 / Num. measured all: 45107 / Num. unique obs: 3879 / CC1/2: 0.677 / Rpim(I) all: 0.473 / Rrim(I) all: 1.606 / Χ2: 0.21 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→82.65 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.83 / SU B: 30.2 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.521 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25239 1444 4.9 %RANDOM
Rwork0.191 ---
obs0.19402 27994 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.613 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å2-0.6 Å2
2--2.24 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: 1 / Resolution: 2.7→82.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4942 568 25 19 5554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125714
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165226
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.6717849
X-RAY DIFFRACTIONr_angle_other_deg0.521.57512054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2165633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.653545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48610905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.2875
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021236
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2473.5132535
X-RAY DIFFRACTIONr_mcbond_other3.233.5142535
X-RAY DIFFRACTIONr_mcangle_it5.0066.33167
X-RAY DIFFRACTIONr_mcangle_other5.0056.3013168
X-RAY DIFFRACTIONr_scbond_it4.3983.9163179
X-RAY DIFFRACTIONr_scbond_other4.1683.8783159
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4136.934653
X-RAY DIFFRACTIONr_long_range_B_refined8.42534.396490
X-RAY DIFFRACTIONr_long_range_B_other8.42434.46491
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 108 -
Rwork0.393 2043 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1737-0.35020.32652.46810.00641.92960.0384-0.06490.02780.148-0.02490.05940.132-0.1308-0.01350.35690.0039-0.07230.2794-0.02550.21759.420466.168771.039
21.88510.4333-0.08272.943-0.75632.6872-0.00030.0979-0.1008-0.00530.00390.09860.2162-0.318-0.00360.31570.0455-0.15560.3108-0.13020.3156-2.284664.189152.9865
33.8383-0.3564-1.34470.23410.1020.59070.1565-0.40830.41210.2875-0.0443-0.048-0.1381-0.1029-0.11230.4995-0.0489-0.10620.6465-0.02850.532852.92775.127140.746
42.1915-0.446-1.49241.10411.98063.93580.0904-0.1757-0.1412-0.0006-0.18850.1022-0.1216-0.44080.0980.43760.0558-0.0240.38530.04440.311238.269857.624423.9139
54.93261.67260.32564.69510.10190.50120.111-0.0265-0.0241-0.097-0.3004-0.3165-0.1121-0.11830.18940.4656-0.0261-0.10060.12390.05060.265156.293362.008524.1223
63.30191.21860.12813.90550.11891.65080.1154-0.7766-0.13860.011-0.2483-0.34360.22-0.05190.13280.4129-0.0509-0.13080.20020.09730.345757.205561.113426.3204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 259
2X-RAY DIFFRACTION2B51 - 259
3X-RAY DIFFRACTION3C2 - 108
4X-RAY DIFFRACTION4D2 - 108
5X-RAY DIFFRACTION5E1 - 14
6X-RAY DIFFRACTION6F1 - 14

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