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- PDB-5ckt: Crystal Structure of KorA, a plasmid-encoded, global transcriptio... -

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Basic information

Entry
Database: PDB / ID: 5ckt
TitleCrystal Structure of KorA, a plasmid-encoded, global transcription regulator
Components(TrfB transcriptional repressor protein) x 2
KeywordsTRANSCRIPTION / Helix-turn-helix
Function / homologyArc Repressor Mutant, subunit A - #2690 / TrfB transcriptional repressor protein / TrfB plasmid transcriptional repressor / Arc Repressor Mutant, subunit A / DNA binding / Orthogonal Bundle / Mainly Alpha / ACETATE ION / TrfB transcriptional repressor protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
Model detailsapo form
AuthorsWhite, S.A. / Hyde, E.I. / Lovering, A.L.
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 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: TrfB transcriptional repressor protein
D: TrfB transcriptional repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5556
Polymers44,4374
Non-polymers1182
Water3,891216
1
A: TrfB transcriptional repressor protein
D: TrfB transcriptional repressor protein


Theoretical massNumber of molelcules
Total (without water)22,3612
Polymers22,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-18 kcal/mol
Surface area11910 Å2
MethodPISA
2
B: TrfB transcriptional repressor protein
C: TrfB transcriptional repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1934
Polymers22,0752
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-17 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.580, 49.690, 52.330
Angle α, β, γ (deg.)98.090, 93.870, 106.010
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 11037.534 Da / Num. of mol.: 3 / 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: Protein TrfB transcriptional repressor protein / Regulatory protein KorA


Mass: 11323.908 Da / Num. of mol.: 1 / 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
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: PEG 4000, sodium acetate, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→27.17 Å / Num. obs: 26649 / % possible obs: 97.2 % / Redundancy: 3.9 % / Rsym value: 0.031 / Net I/σ(I): 26.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3.6 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
SOLVEphasing
RefinementResolution: 2→27.17 Å / FOM work R set: 0.8268 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 2704 5.11 %Random selection
Rwork0.1958 50230 --
obs0.1972 52934 96.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.3 Å2 / Biso mean: 55.86 Å2 / Biso min: 18.84 Å2
Refinement stepCycle: final / Resolution: 2→27.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3074 0 8 216 3298
Biso mean--41.84 48.25 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043165
X-RAY DIFFRACTIONf_angle_d0.8124277
X-RAY DIFFRACTIONf_chiral_restr0.043476
X-RAY DIFFRACTIONf_plane_restr0.003559
X-RAY DIFFRACTIONf_dihedral_angle_d15.5421192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9979-2.03420.30651230.29882466258990
2.0342-2.07330.32911730.28262603277697
2.0733-2.11570.26571240.26842669279395
2.1157-2.16160.31881540.26142666282096
2.1616-2.21190.27971480.24692531267997
2.2119-2.26720.2791330.23292721285496
2.2672-2.32850.21881460.22952670281697
2.3285-2.3970.22851140.20642665277996
2.397-2.47430.22551550.20432653280897
2.4743-2.56270.26511180.20722634275297
2.5627-2.66520.27191330.21442704283796
2.6652-2.78640.21841400.21022667280798
2.7864-2.93320.26271220.21792690281297
2.9332-3.11680.26221630.20632671283497
3.1168-3.35710.25061190.21712648276797
3.3571-3.69440.20121420.18752675281797
3.6944-4.22760.19181630.16042664282797
4.2276-5.32120.18791850.16172640282597
5.3212-29.34670.18861490.17132593274295
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)
12.66731.0445-0.37866.9347-0.26824.8382-0.0487-1.05220.08380.61930.1923-0.574-0.22450.2333-0.21450.34380.0931-0.02150.6763-0.08560.23317.0833.62636.2275
24.902-0.7823-0.05723.809-2.07115.7199-0.08320.4593-0.3182-0.6135-0.20550.03150.22230.41930.21440.29270.0083-0.00390.2423-0.04210.1617-1.3544-0.3272-18.1772
35.4045-1.36612.99056.8235-4.98058.4992-0.0470.2180.7910.41830.04030.2905-0.5776-0.0649-0.01530.5739-0.0602-0.01790.24090.07930.4728.1496-25.2207-28.6619
40.34970.65480.28553.6294-1.81083.92540.0092-0.6243-1.2777-0.16830.27720.1620.45750.0109-0.16530.34470.04480.00390.43030.31230.8203-4.002-19.0641-1.0101
51.98880.28760.16864.8916-0.1974.07910.1883-0.5922-0.40980.5411-0.12270.76330.5188-0.2268-0.06230.36310.03350.13250.52250.19930.630122.7258-10.25222.0235
67.0605-2.00631.64673.7206-0.83037.86880.66870.66420.5142-0.58790.06330.3349-0.0491-0.7579-0.60230.43210.01790.00430.51720.19370.871523.6452-6.8543-23.0728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq :65)A1 - 65
2X-RAY DIFFRACTION2(chain B and resseq :65)B1 - 65
3X-RAY DIFFRACTION3(chain C and resseq :65)C1 - 65
4X-RAY DIFFRACTION4(chain D and resseq :65)D3 - 65
5X-RAY DIFFRACTION5((chain A or chain D) and resseq 66:)A0
6X-RAY DIFFRACTION6((chain B or chain C) and resseq 66:)B0

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