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- PDB-5cm3: Crystal Structure of KorA, a plasmid-encoded, global transcriptio... -

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Basic information

Entry
Database: PDB / ID: 5cm3
TitleCrystal Structure of KorA, a plasmid-encoded, global transcription regulator
Components
  • 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'
  • TrfB transcriptional repressor protein
KeywordsTRANSCRIPTION / Helix-turn-helix / DNA 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: 2.302 Å
Model detailsKorA:DNA complexes
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 1.2Jan 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'


Theoretical massNumber of molelcules
Total (without water)33,8814
Polymers33,8814
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-57 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.540, 115.100, 49.930
Angle α, β, γ (deg.)90.000, 113.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TrfB transcriptional repressor protein / Regulatory protein KorA / A6H992 P03052 KorA repressor protein


Mass: 10807.316 Da / Num. of mol.: 2 / Fragment: KorA, UNP resiodues 1-97
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 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.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: PEG 6000, 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: 2.3→23.46 Å / Num. obs: 19920 / % possible obs: 97.6 % / Redundancy: 1.9 % / Net I/σ(I): 17.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.032 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CKT, theoretical model of DNA

5ckt


Resolution: 2.302→23.459 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 995 5 %Random selection
Rwork0.1931 18887 --
obs0.1951 19882 97.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.52 Å2 / Biso mean: 60.4469 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.302→23.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 778 0 139 2403
Biso mean---54.42 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112413
X-RAY DIFFRACTIONf_angle_d1.4823428
X-RAY DIFFRACTIONf_chiral_restr0.064383
X-RAY DIFFRACTIONf_plane_restr0.006309
X-RAY DIFFRACTIONf_dihedral_angle_d23.895954
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3023-2.42360.30661340.27762548268293
2.4236-2.57520.28791560.25942710286698
2.5752-2.77380.29091510.2452747289899
2.7738-3.05240.28691480.23422724287299
3.0524-3.49280.24331310.19622729286099
3.4928-4.39580.21371540.16572750290499
4.3958-23.460.17541210.15862679280095
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)
14.7354-3.0153-0.00832.0538-1.38467.7965-0.24120.46970.73770.22890.3129-0.4786-0.4908-0.72110.22320.44970.1277-0.01850.88590.04320.5796-18.029311.60958.7061
29.47750.70492.84592.2699-1.5452.8890.2368-1.2204-0.82020.7412-0.10250.25140.2717-1.1355-0.05890.5178-0.01290.09150.66850.09020.4412-12.31130.192911.063
31.89460.959-0.0172.2137-0.26822.4002-0.0405-0.16530.1720.0814-0.17860.0233-0.2396-0.630.1690.43340.0887-0.03060.5699-0.03880.341-7.57339.77129.7958
46.8831-0.3935-1.86736.14652.80481.62990.4409-0.54360.75530.2031-0.5680.02780.87411.0185-0.13950.40370.0053-0.13231.11690.09690.3006-20.26794.6795-10.2717
52.7322-0.0722-0.58742.89560.6052.9354-0.01160.21560.88250.3219-0.1996-0.7528-0.84840.62280.37390.6295-0.1827-0.12591.15210.05570.523-14.172611.1021-22.2903
60.1626-0.28710.49111.2432-0.49992.50240.53340.2177-0.43451.52470.0765-0.11970.8422-0.3229-0.13241.1698-0.2140.23940.9559-0.11561.14466.7808-16.9429-15.334
74.16070.7104-0.06563.46081.12715.7744-0.2370.5713-0.3631-0.2490.3093-0.25020.17690.6719-0.06280.41850.02620.04930.66040.00710.531114.1049-6.4216-13.655
84.4971-0.74410.29734.26220.37174.45480.02730.4971-0.57980.3041-0.21230.01570.36510.23690.15180.4078-0.00910.06920.4305-0.00460.54088.7132-7.9337-7.732
91.0771.1302-0.25441.0490.55292.2165-0.7064-1.1293-0.6821-0.2050.1030.09480.41050.84710.06020.3184-0.0205-0.08381.04550.14290.3988-13.61591.618-20.8983
102.93731.2293-0.7772.12043.56049.5733-0.03550.0152-1.78850.0454-0.2635-0.24971.68631.37-0.6050.60940.09750.00460.8170.00370.6676-14.9476-4.04-25.8572
111.73592.9322-1.54795.0573-2.08093.94370.6117-0.48050.68180.3001-1.09-1.2885-0.29270.67860.0061.0728-0.0194-0.06730.48610.05191.04954.160625.97127.8996
122.4407-0.08280.15861.5833-0.70920.42990.20690.12250.63230.1321-0.1535-0.3636-0.63990.01460.31640.60070.1021-0.00130.39580.05330.49770.037512.77811.342
134.5677-0.3225-0.6744.1713-0.28081.02550.2916-0.22570.0384-0.0595-0.439-1.2971-0.10110.0820.23790.676-0.00450.04570.40220.00180.62647.8935-1.21840.4898
142.4296-0.243-0.71625.96524.92535.50890.0473-0.9361-1.53040.9676-1.8510.08171.48060.02250.81160.9256-0.18660.13880.52850.1110.57980.1199-13.42757.2017
154.676-0.46142.71315.3605-2.05752.63330.48031.0855-0.82080.1981-1.1120.03640.8128-0.06060.14870.82780.05630.12020.4663-0.12431.056-1.3074-23.1307-4.8616
161.03440.8247-0.51711.1986-1.67013.14560.8865-0.7804-0.4030.8124-1.4004-0.3041-0.02280.62570.54330.9818-0.08740.12350.48840.12421.41875.9265-26.21651.6185
173.1375-2.19530.35054.58242.22475.72810.0635-0.3026-1.0528-0.4869-0.2388-0.12740.2925-0.08890.32460.6896-0.05360.17150.3134-0.01150.70970.9824-12.4122-2.3151
181.49210.4312-0.34462.38720.39832.2004-0.0418-0.13110.18870.0956-0.2827-0.49370.5004-0.00150.23210.55690.02510.05930.32480.0390.55731.02150.52367.0836
192.80860.5638-0.6923.3932.75672.93360.8248-0.2305-0.1088-0.1866-0.7726-0.8814-1.49220.45110.18970.3362-0.0876-0.01360.4580.06240.86289.488912.97341.6805
201.06870.80562.0637.27772.20917.33650.14130.34130.6628-0.3569-1.11160.2603-0.0587-1.32930.77861.09620.0560.13630.5122-0.12630.7871-1.741723.00370.2841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:12)A1 - 12
2X-RAY DIFFRACTION2(chain A and resid 13:25)A13 - 25
3X-RAY DIFFRACTION3(chain A and resid 26:65)A26 - 65
4X-RAY DIFFRACTION4(chain A and resid 66:76)A66 - 76
5X-RAY DIFFRACTION5(chain A and resid 77:97)A77 - 97
6X-RAY DIFFRACTION6(chain B and resid 1:4)B1 - 4
7X-RAY DIFFRACTION7(chain B and resid 5:39)B5 - 39
8X-RAY DIFFRACTION8(chain B and resid 40:65)B40 - 65
9X-RAY DIFFRACTION9(chain B and resid 66:87)B66 - 87
10X-RAY DIFFRACTION10(chain B and resid 88:93)B88 - 93
11X-RAY DIFFRACTION11(chain C and resid 1:4)C1 - 4
12X-RAY DIFFRACTION12(chain C and resid 5:8)C5 - 8
13X-RAY DIFFRACTION13(chain C and resid 9:12)C9 - 12
14X-RAY DIFFRACTION14(chain C and resid 13:16)C13 - 16
15X-RAY DIFFRACTION15(chain C and resid 17:20)C17 - 20
16X-RAY DIFFRACTION16(chain D and resid 1:4)D1 - 4
17X-RAY DIFFRACTION17(chain D and resid 5:8)D5 - 8
18X-RAY DIFFRACTION18(chain D and resid 9:12)D9 - 12
19X-RAY DIFFRACTION19(chain D and resid 13:16)D13 - 16
20X-RAY DIFFRACTION20(chain D and resid 17:20)D17 - 20

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