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- PDB-5clv: Crystal Structure of KorA-operator DNA complex (KorA-OA) -

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Basic information

Entry
Database: PDB / ID: 5clv
TitleCrystal Structure of KorA-operator DNA complex (KorA-OA)
Components
  • (TrfB transcriptional repressor protein) x 2
  • 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'
KeywordsTRANSCRIPTION / Helix-turn-helix / complex
Function / homologyTrfB transcriptional repressor protein / TrfB plasmid transcriptional repressor / DNA binding / DNA / DNA (> 10) / TrfB transcriptional repressor protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
Model detailsapo form
AuthorsWhite, S.A. / Hyde, E.I. / Rajasekar, K.V.
Citation
Journal: Nucleic Acids Res. / Year: 2016
Title: Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator.
Authors: Rajasekar, K.V. / Lovering, A.L. / Dancea, F. / Scott, D.J. / Harris, S.A. / Bingle, L.E. / Roessle, M. / Thomas, C.M. / Hyde, E.I. / White, S.A.
#1: Journal: Mol. Microbiol. / Year: 2008
Title: A single aromatic residue in transcriptional repressor protein KorA is critical for cooperativity with its co-regulator KorB.
Authors: Bingle, L.E. / Rajasekar, K.V. / Muntaha, S.t. / Nadella, V. / Hyde, E.I. / Thomas, C.M.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Sep 11, 2019Group: Data collection / Refinement description / Category: refine_ls_shell / Item: _refine_ls_shell.R_factor_R_free
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TrfB transcriptional repressor protein
B: TrfB transcriptional repressor protein
C: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'
D: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'
E: TrfB transcriptional repressor protein
F: TrfB transcriptional repressor protein
G: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'
H: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'
I: TrfB transcriptional repressor protein
J: TrfB transcriptional repressor protein
K: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'
L: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'
M: TrfB transcriptional repressor protein
N: TrfB transcriptional repressor protein
O: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'
P: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'


Theoretical massNumber of molelcules
Total (without water)112,96216
Polymers112,96216
Non-polymers00
Water2,954164
1
A: TrfB transcriptional repressor protein
B: TrfB transcriptional repressor protein
C: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'
D: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'


Theoretical massNumber of molelcules
Total (without water)33,6184
Polymers33,6184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-54 kcal/mol
Surface area16510 Å2
MethodPISA
2
E: TrfB transcriptional repressor protein
F: TrfB transcriptional repressor protein
G: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'
H: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'


Theoretical massNumber of molelcules
Total (without water)26,4484
Polymers26,4484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-39 kcal/mol
Surface area12570 Å2
MethodPISA
3
I: TrfB transcriptional repressor protein
J: TrfB transcriptional repressor protein
K: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'
L: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'


Theoretical massNumber of molelcules
Total (without water)26,4484
Polymers26,4484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-38 kcal/mol
Surface area12230 Å2
MethodPISA
4
M: TrfB transcriptional repressor protein
N: TrfB transcriptional repressor protein
O: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'
P: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'


Theoretical massNumber of molelcules
Total (without water)26,4484
Polymers26,4484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-39 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.460, 114.030, 82.070
Angle α, β, γ (deg.)90.000, 99.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TrfB transcriptional repressor protein / Regulatory protein KorA


Mass: 10676.119 Da / Num. of mol.: 2 / Fragment: KorA
Source method: isolated from a genetically manipulated source
Details: IncP-1 plasmid RK2 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trfB, korA / Plasmid: pET28a / Details (production host): derivative pGBT340 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03052
#2: DNA chain
5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'


Mass: 6132.991 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Protein
TrfB transcriptional repressor protein / Regulatory protein KorA


Mass: 7090.981 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: IncP-1 plasmid RK2 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trfB, korA / Plasmid: pET28a / Details (production host): derivative pGBT340 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03052
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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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: 3.29 Å3/Da / Density % sol: 62.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: PEG 4000, sodium acetate, ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.5→25.05 Å / Num. obs: 49516 / % possible obs: 97.9 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 12.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CKT, theoretical DNA model

5ckt


Resolution: 2.5→25.047 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 33.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2924 4619 5.4 %thin shells
Rwork0.2792 80861 --
obs0.2798 85480 85.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.44 Å2 / Biso mean: 38.4617 Å2 / Biso min: 11.43 Å2
Refinement stepCycle: final / Resolution: 2.5→25.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4415 3112 0 164 7691
Biso mean---28.43 -
Num. residues----732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037971
X-RAY DIFFRACTIONf_angle_d0.79711419
X-RAY DIFFRACTIONf_chiral_restr0.0421298
X-RAY DIFFRACTIONf_plane_restr0.005942
X-RAY DIFFRACTIONf_dihedral_angle_d24.4283155
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.52840.755220.34453106310894
2.5284-2.55810.335308694
2.5581-2.58930.3505313493
2.5893-2.6220.37685530.35152501305494
2.622-2.65650.537456517
2.6565-2.69280.5051222167
2.6928-2.73130.42832870.5436799108633
2.7313-2.7720.48012820.37572895317794
2.772-2.81520.3655314095
2.8152-2.86130.3504308994
2.8613-2.91060.39714710.33662684315595
2.9106-2.96340.3274311395
2.9634-3.02030.38094300.33842710314094
3.0203-3.08190.3231315995
3.0819-3.14880.3167308395
3.1488-3.22190.35644060.28552767317395
3.2219-3.30230.2772311694
3.3023-3.39130.29043250.28182639296489
3.3913-3.49090.3696224368
3.4909-3.60330.32813370.29782648298590
3.6033-3.73160.3438227368
3.7316-3.88050.30452530.26682447270082
3.8805-4.05640.250440.28962590259479
4.0564-4.26930.232150.22782979319496
4.2693-4.53530.24662150.20962977319296
4.5353-4.88310.24211960.232952314896
4.8831-5.37010.24291480.21813086323496
5.3701-6.13720.22741380.21693025316396
6.1372-7.69490.19391800.20313009318996
7.6949-25.04830.24411770.21912825300290

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