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- PDB-8qa8: Crystal structure of the C-terminally truncated transcriptional r... -

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Basic information

Entry
Database: PDB / ID: 8qa8
TitleCrystal structure of the C-terminally truncated transcriptional repressor protein KorB from the RK2 plasmid complexed with CTP-gamma-S
ComponentsTranscriptional repressor protein KorB
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 / : / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin ...KorB, C-terminal / Repressor KorB domain / KorB, C-terminal domain superfamily / KorB DNA-binding domain / KorB C-terminal beta-barrel domain / KorB domain / : / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / Transcriptional repressor, C-terminal
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / Transcriptional repressor protein KorB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Transcriptional repressor protein KorB
D: Transcriptional repressor protein KorB
E: Transcriptional repressor protein KorB
F: Transcriptional repressor protein KorB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,19034
Polymers158,5116
Non-polymers3,67928
Water3,675204
1
A: Transcriptional repressor protein KorB
B: Transcriptional repressor protein KorB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,08712
Polymers52,8372
Non-polymers1,25010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-78 kcal/mol
Surface area20480 Å2
MethodPISA
2
C: Transcriptional repressor protein KorB
D: Transcriptional repressor protein KorB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,05211
Polymers52,8372
Non-polymers1,2149
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-70 kcal/mol
Surface area20240 Å2
MethodPISA
3
E: Transcriptional repressor protein KorB
F: Transcriptional repressor protein KorB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,05211
Polymers52,8372
Non-polymers1,2149
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-69 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.686, 152.710, 198.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Transcriptional repressor protein KorB


Mass: 26418.576 Da / Num. of mol.: 6
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: Chemical
ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.89 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9179 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 2.3→198.27 Å / Num. obs: 80304 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.067 / Rrim(I) all: 0.245 / Χ2: 0.43 / Net I/σ(I): 7.9 / Num. measured all: 1069894
Reflection shellResolution: 2.3→2.35 Å / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 1.887 / Num. measured all: 50482 / Num. unique obs: 4563 / CC1/2: 0.718 / Rpim(I) all: 0.594 / Rrim(I) all: 1.979 / Χ2: 0.18 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→121.28 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.922 / SU B: 20.803 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25619 4000 5 %RANDOM
Rwork0.2274 ---
obs0.22881 76214 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: 55.721 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2---0.97 Å20 Å2
3---0.43 Å2
Refinement stepCycle: 1 / Resolution: 2.3→121.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9414 0 196 204 9814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0129958
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169384
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.66113548
X-RAY DIFFRACTIONr_angle_other_deg0.4691.57921651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8451229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.797587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.229101708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.21495
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211864
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022223
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_it1.8322.0894883
X-RAY DIFFRACTIONr_mcbond_other1.8312.094883
X-RAY DIFFRACTIONr_mcangle_it2.9583.7436123
X-RAY DIFFRACTIONr_mcangle_other2.9583.7436124
X-RAY DIFFRACTIONr_scbond_it2.5522.2865075
X-RAY DIFFRACTIONr_scbond_other2.5422.2865064
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1454.097426
X-RAY DIFFRACTIONr_long_range_B_refined6.15619.3310842
X-RAY DIFFRACTIONr_long_range_B_other6.15419.310825
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 269 -
Rwork0.349 5607 -
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)
13.07521.3186-0.08713.0082-0.80171.54960.03390.10.33130.0814-0.04810.1075-0.2313-0.0160.01420.03810.0392-0.00120.5064-0.0210.040528.8652-8.1322.4792
23.2651-1.0706-1.32131.89250.73092.97620.0231-0.1420.28940.01480.0431-0.112-0.290.0756-0.06610.0384-0.0404-0.00880.4612-0.0320.064827.3244-12.936815.3856
31.94690.0584-0.4092.1261-0.15233.2863-0.00290.1063-0.0563-0.1470.0873-0.00120.14310.0485-0.08440.0172-0.01260.00010.46840.05580.226275.56963.0234-23.6505
43.54590.8731-0.35822.3109-0.67912.32590.02120.21220.2254-0.25530.0240.2163-0.0607-0.1087-0.04520.05730.07470.0210.62310.08610.147861.7566.5759-22.621
52.33160.7216-0.41313.1404-0.56093.53270.00220.0145-0.36960.0941-0.03740.03730.3095-0.09590.03520.04830.0254-0.02820.4916-0.09910.147939.2539-21.432443.139
63.5553-0.7026-1.48931.67010.55454.0219-0.0719-0.0345-0.35650.0004-0.0258-0.140.31760.11030.09770.0596-0.0202-0.0330.45580.00850.153553.0411-17.36344.2564
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 252
2X-RAY DIFFRACTION2B52 - 253
3X-RAY DIFFRACTION3C52 - 251
4X-RAY DIFFRACTION4D52 - 252
5X-RAY DIFFRACTION5E52 - 251
6X-RAY DIFFRACTION6F52 - 248

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