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- PDB-4nhj: Crystal structure of Klebsiella pneumoniae RstA DNA-binding domai... -

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Basic information

Entry
Database: PDB / ID: 4nhj
TitleCrystal structure of Klebsiella pneumoniae RstA DNA-binding domain in complex with RstA box
Components
  • 5'-D(*CP*AP*GP*GP*GP*AP*GP*TP*AP*AP*CP*GP*GP*AP*AP*TP*GP*TP*AP*CP*AP*AP*C)-3'
  • 5'-D(*GP*GP*TP*TP*GP*TP*AP*CP*AP*TP*TP*CP*CP*GP*TP*TP*AP*CP*TP*CP*CP*CP*T)-3'
  • DNA-binding transcriptional regulator RstA
KeywordsTRANSCRIPTION REGULATOR/DNA / Two-Component System / response regulator / TRANSCRIPTION REGULATOR-DNA complex
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Response regulator (Activator) in two-component regulatory system with RstB (OmpR family) / :
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.701 Å
AuthorsLi, Y.C. / Hsiao, C.D.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element.
Authors: Li, Y.C. / Chang, C.K. / Chang, C.F. / Cheng, Y.H. / Fang, P.J. / Yu, T. / Chen, S.C. / Li, Y.C. / Hsiao, C.D. / Huang, T.H.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: DNA-binding transcriptional regulator RstA
B: DNA-binding transcriptional regulator RstA
C: 5'-D(*GP*GP*TP*TP*GP*TP*AP*CP*AP*TP*TP*CP*CP*GP*TP*TP*AP*CP*TP*CP*CP*CP*T)-3'
D: 5'-D(*CP*AP*GP*GP*GP*AP*GP*TP*AP*AP*CP*GP*GP*AP*AP*TP*GP*TP*AP*CP*AP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)41,1124
Polymers41,1124
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-28 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.935, 33.313, 72.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA-binding transcriptional regulator RstA / RstA protein


Mass: 13495.427 Da / Num. of mol.: 2 / Fragment: UNP residues 131-239 / Mutation: L153M,L168M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: rstA, KPN2242_10390, KPR_2822 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0GNT0, UniProt: A6T8N1*PLUS
#2: DNA chain 5'-D(*GP*GP*TP*TP*GP*TP*AP*CP*AP*TP*TP*CP*CP*GP*TP*TP*AP*CP*TP*CP*CP*CP*T)-3'


Mass: 6973.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RstA box leading strand
#3: DNA chain 5'-D(*CP*AP*GP*GP*GP*AP*GP*TP*AP*AP*CP*GP*GP*AP*AP*TP*GP*TP*AP*CP*AP*AP*C)-3'


Mass: 7147.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RstA box lagging strand
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Bis-Tris, 28% PEG400, 1.32 M sodium formate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 299K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.96357, 0.97879, 0.97862
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2012
RadiationMonochromator: LN2-cooled, fixed-exit double crystal Si(111)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.963571
20.978791
30.978621
ReflectionResolution: 2.7→50 Å / Num. all: 11334 / Num. obs: 10418 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 60.32
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 10 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 7.2 / % possible all: 82.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.701→25.03 Å / SU ML: 0.4 / σ(F): 1.35 / Phase error: 30.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2713 1039 10.01 %RANDOM
Rwork0.216 ---
obs0.2217 10378 91.74 %-
all-10378 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.452 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.682 Å2-0 Å2-0 Å2
2--11.26 Å20 Å2
3----20.9421 Å2
Refinement stepCycle: LAST / Resolution: 2.701→25.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1601 918 0 63 2582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042656
X-RAY DIFFRACTIONf_angle_d0.9483779
X-RAY DIFFRACTIONf_dihedral_angle_d22.8181055
X-RAY DIFFRACTIONf_chiral_restr0.06430
X-RAY DIFFRACTIONf_plane_restr0.003326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.701-2.84350.35711310.33341180X-RAY DIFFRACTION84
2.8435-3.02140.37181350.28361213X-RAY DIFFRACTION84
3.0214-3.25420.31491390.24851247X-RAY DIFFRACTION88
3.2542-3.58090.31971440.24641293X-RAY DIFFRACTION91
3.5809-4.09710.26491560.21831405X-RAY DIFFRACTION95
4.0971-5.15450.26371590.18581436X-RAY DIFFRACTION98
5.1545-25.03090.22351750.191565X-RAY DIFFRACTION100

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