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- PDB-5dcm: Structure of a lantibiotic response regulator: C-terminal domain ... -

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Basic information

Entry
Database: PDB / ID: 5dcm
TitleStructure of a lantibiotic response regulator: C-terminal domain of the nisin resistance regulator NsrR
Components(PhoB family transcriptional regulator) x 2
KeywordsSIGNALING PROTEIN / Antimicrobial peptide / lantibiotic / nisin / resistance/regulation / two component system
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / 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-binding response regulator
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsKhosa, S. / Kleinschrodt, D. / Hoeppner, A. / Smits, S.H.J.
CitationJournal: Plos One / Year: 2016
Title: Structure of the Response Regulator NsrR from Streptococcus agalactiae, Which Is Involved in Lantibiotic Resistance.
Authors: Khosa, S. / Hoeppner, A. / Gohlke, H. / Schmitt, L. / Smits, S.H.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 2.0May 8, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.occupancy / _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: PhoB family transcriptional regulator
B: PhoB family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)55,5142
Polymers55,5142
Non-polymers00
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-5 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.380, 60.460, 56.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-369-

HOH

21B-401-

HOH

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Components

#1: Protein PhoB family transcriptional regulator


Mass: 27756.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: DK41_05180, EN72_05470 / Production host: Escherichia coli (E. coli) / References: UniProt: X5JZS1
#2: Protein PhoB family transcriptional regulator


Mass: 27756.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: DK41_05180, EN72_05470 / Production host: Escherichia coli (E. coli) / References: UniProt: X5JZS1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: 0.1 M SPG buffer pH 8.0 and 25% (w/v) PEG 1500 / PH range: 6.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07145 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07145 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 124813 / % possible obs: 98.8 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→56.85 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 3740 7.63 %
Rwork0.1868 --
obs0.1893 49037 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→56.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 0 325 1877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071576
X-RAY DIFFRACTIONf_angle_d1.092129
X-RAY DIFFRACTIONf_dihedral_angle_d13.286593
X-RAY DIFFRACTIONf_chiral_restr0.043255
X-RAY DIFFRACTIONf_plane_restr0.006266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6002-1.62040.25351300.23511711X-RAY DIFFRACTION99
1.6204-1.64170.27061290.21711656X-RAY DIFFRACTION99
1.6417-1.66420.24551230.22411738X-RAY DIFFRACTION99
1.6642-1.6880.22361660.22541643X-RAY DIFFRACTION100
1.688-1.71320.27371420.20991703X-RAY DIFFRACTION99
1.7132-1.740.19941440.22351655X-RAY DIFFRACTION100
1.74-1.76850.28131440.20631699X-RAY DIFFRACTION99
1.7685-1.7990.25521260.21571657X-RAY DIFFRACTION99
1.799-1.83170.23551520.2061697X-RAY DIFFRACTION99
1.8317-1.86690.18481140.21251670X-RAY DIFFRACTION99
1.8669-1.90510.21721350.20431678X-RAY DIFFRACTION98
1.9051-1.94650.22581560.19711639X-RAY DIFFRACTION98
1.9465-1.99180.26111040.17971658X-RAY DIFFRACTION97
1.9918-2.04160.20471420.19121654X-RAY DIFFRACTION97
2.0416-2.09680.24171530.18811640X-RAY DIFFRACTION98
2.0968-2.15850.2191390.18121691X-RAY DIFFRACTION99
2.1585-2.22820.23921260.19271700X-RAY DIFFRACTION99
2.2282-2.30780.25991430.19171649X-RAY DIFFRACTION99
2.3078-2.40020.22611510.18611674X-RAY DIFFRACTION100
2.4002-2.50940.2111480.19491728X-RAY DIFFRACTION100
2.5094-2.64170.22951390.18591678X-RAY DIFFRACTION100
2.6417-2.80720.20771450.18911669X-RAY DIFFRACTION100
2.8072-3.0240.2991300.19011684X-RAY DIFFRACTION99
3.024-3.32830.18581440.18681703X-RAY DIFFRACTION99
3.3283-3.80980.19221450.17421637X-RAY DIFFRACTION97
3.8098-4.79950.17691380.14631683X-RAY DIFFRACTION100
4.7995-56.88590.21091320.18691703X-RAY DIFFRACTION100

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