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- PDB-4kny: Crystal structure of the response regulator KdpE complexed to DNA... -

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Basic information

Entry
Database: PDB / ID: 4kny
TitleCrystal structure of the response regulator KdpE complexed to DNA in an active-like conformation
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: 2.945 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
DepositionMay 10, 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)69,4344
Polymers69,4344
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-44 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.140, 133.140, 133.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein KDP operon transcriptional regulatory protein KdpE


Mass: 25495.242 Da / Num. of mol.: 2 / Fragment: UNP residues 3-225
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.: 25 / 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: 4.27 Å3/Da / Density % sol: 71.16 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10-15% PEG 4K, 0.1 M sodium acetate buffer (pH 5.5), 0.1 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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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: 2.95→66.57 Å / Num. all: 26044 / Num. obs: 25980 / % possible obs: 99.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Net I/σ(I): 12.1
Reflection shellResolution: 2.95→3.05 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 3.8 / % 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: PDB entry 1ZH4, 3ZQ7

1zh4

3zq7


Resolution: 2.945→66.57 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 2011 7.74 %Random
Rwork0.2086 ---
obs0.2116 25980 99.8 %-
all-26044 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.945→66.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 981 0 25 4562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034718
X-RAY DIFFRACTIONf_angle_d0.7636590
X-RAY DIFFRACTIONf_dihedral_angle_d19.5371843
X-RAY DIFFRACTIONf_chiral_restr0.046748
X-RAY DIFFRACTIONf_plane_restr0.003691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9451-3.01880.38631380.30031672X-RAY DIFFRACTION100
3.0188-3.10040.29771430.27431695X-RAY DIFFRACTION100
3.1004-3.19160.28861460.25551669X-RAY DIFFRACTION100
3.1916-3.29470.33741410.25581679X-RAY DIFFRACTION100
3.2947-3.41240.3271430.26831692X-RAY DIFFRACTION100
3.4124-3.5490.25651400.23521698X-RAY DIFFRACTION100
3.549-3.71050.25811400.2171698X-RAY DIFFRACTION100
3.7105-3.90610.28981410.20851696X-RAY DIFFRACTION100
3.9061-4.15080.22071410.19771707X-RAY DIFFRACTION100
4.1508-4.47130.2131460.18471715X-RAY DIFFRACTION100
4.4713-4.92110.22241440.17221722X-RAY DIFFRACTION100
4.9211-5.63290.22711450.19651741X-RAY DIFFRACTION100
5.6329-7.09550.28481490.22741763X-RAY DIFFRACTION100
7.0955-66.5870.20041540.18211822X-RAY DIFFRACTION97

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