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- PDB-4kfc: Crystal structure of a hyperactive mutant of response regulator K... -

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Basic information

Entry
Database: PDB / ID: 4kfc
TitleCrystal structure of a hyperactive mutant of response regulator KdpE complexed to its promoter DNA
Components
  • (Promoter DNA) x 2
  • KDP operon transcriptional regulatory protein KdpE
KeywordsTRANSCRIPTION REGULATOR/DNA / receiver domain / DNA-binding domain / TRANSCRIPTION REGULATOR-DNA complex
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / protein homodimerization activity / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / KDP operon transcriptional regulatory protein KdpE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsKumar, S. / Narayanan, A. / Yernool, D.A.
CitationJournal: Nat Commun / Year: 2014
Title: An asymmetric heterodomain interface stabilizes a response regulator-DNA complex.
Authors: Narayanan, A. / Kumar, S. / Evrard, A.N. / Paul, L.N. / Yernool, D.A.
History
DepositionApr 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KDP operon transcriptional regulatory protein KdpE
B: KDP operon transcriptional regulatory protein KdpE
Y: Promoter DNA
Z: Promoter DNA


Theoretical massNumber of molelcules
Total (without water)69,3184
Polymers69,3184
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-55 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.770, 132.770, 134.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe present structures with two protein molecules bound to dsDNA, represents the biological assemble.

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Components

#1: Protein KDP operon transcriptional regulatory protein KdpE


Mass: 25437.207 Da / Num. of mol.: 2 / Fragment: UNP residues 3-225 / Mutation: E216A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0694, JW5096, kdpE / Production host: Escherichia coli (E. coli) / References: UniProt: P21866
#2: DNA chain Promoter DNA


Mass: 9025.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED
#3: DNA chain Promoter DNA


Mass: 9418.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 4.28 Å3/Da / Density % sol: 71.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 3-5% PEG 4K, 0.1 M sodium acetate buffer (pH 5.5), 0.1 M MgCl2, 2mM L-proline, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.53→44.43 Å / Num. all: 40355 / Num. obs: 40336 / % possible obs: 99.95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.48
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.4 / Num. unique all: 40355 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERphasing
PHENIX(phenix.refine: dev_1352)refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZH4 and 3ZQ7

1zh4

3zq7


Resolution: 2.53→44.32 Å / SU ML: 0.31 / σ(F): 1.33 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.245 4013 9.95 %Random
Rwork0.2038 ---
obs0.208 40336 99.07 %-
all-40355 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.53→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 1224 0 148 4911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044973
X-RAY DIFFRACTIONf_angle_d0.9286985
X-RAY DIFFRACTIONf_dihedral_angle_d20.7391953
X-RAY DIFFRACTIONf_chiral_restr0.054791
X-RAY DIFFRACTIONf_plane_restr0.003699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.55980.38621290.29521247X-RAY DIFFRACTION100
2.5598-2.5910.29431360.26931257X-RAY DIFFRACTION100
2.591-2.62380.32321430.25441240X-RAY DIFFRACTION100
2.6238-2.65830.2791370.2531240X-RAY DIFFRACTION100
2.6583-2.69470.31981410.24351224X-RAY DIFFRACTION100
2.6947-2.73320.27291360.23861237X-RAY DIFFRACTION100
2.7332-2.7740.32671400.25721244X-RAY DIFFRACTION100
2.774-2.81730.30741370.23741258X-RAY DIFFRACTION100
2.8173-2.86350.32281350.2391248X-RAY DIFFRACTION100
2.8635-2.91290.31641420.24871242X-RAY DIFFRACTION100
2.9129-2.96580.28711310.2481241X-RAY DIFFRACTION100
2.9658-3.02290.35061400.26111245X-RAY DIFFRACTION100
3.0229-3.08450.29591360.25851256X-RAY DIFFRACTION100
3.0845-3.15160.32411430.25791252X-RAY DIFFRACTION100
3.1516-3.22490.2951380.2411249X-RAY DIFFRACTION100
3.2249-3.30550.26711400.23311245X-RAY DIFFRACTION100
3.3055-3.39480.26811390.22621262X-RAY DIFFRACTION100
3.3948-3.49470.26731410.21851258X-RAY DIFFRACTION100
3.4947-3.60750.23111330.21071260X-RAY DIFFRACTION100
3.6075-3.73630.26171340.19551259X-RAY DIFFRACTION100
3.7363-3.88580.23621450.19451259X-RAY DIFFRACTION100
3.8858-4.06260.22281380.1831274X-RAY DIFFRACTION100
4.0626-4.27660.20261400.16371278X-RAY DIFFRACTION100
4.2766-4.54430.17871430.15961270X-RAY DIFFRACTION100
4.5443-4.89480.20041400.15951280X-RAY DIFFRACTION100
4.8948-5.38660.22641460.18091296X-RAY DIFFRACTION100
5.3866-6.16420.23941400.19741295X-RAY DIFFRACTION100
6.1642-7.75950.2211480.19511319X-RAY DIFFRACTION100
7.7595-44.32680.19911220.19251088X-RAY DIFFRACTION77

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