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- PDB-4xyq: Structure of AgrA LytTR domain in complex with promoters -

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Basic information

Entry
Database: PDB / ID: 4xyq
TitleStructure of AgrA LytTR domain in complex with promoters
Components
  • Accessory gene regulator A
  • DNA (5'-D(*AP*AP*TP*AP*CP*TP*TP*AP*AP*CP*TP*GP*TP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*AP*AP*CP*AP*GP*TP*TP*AP*AP*GP*TP*AP*T)-3')
KeywordsDNA/DNA BINDING PROTEIN / Protein-DNA complex / DNA-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA binding / cytoplasm
Similarity search - Function
LytTr DNA-binding domain / : / LytTr DNA-binding domain / LytTr DNA-binding domain / LytTR DNA-binding domain / LytTR-type HTH domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...LytTr DNA-binding domain / : / LytTr DNA-binding domain / LytTr DNA-binding domain / LytTR DNA-binding domain / LytTR-type HTH domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Accessory gene regulator A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsGopal, B. / Rajasree, K.
CitationJournal: Biochem Biophys Rep / Year: 2016
Title: Conformational features of theStaphylococcus aureusAgrA-promoter interactions rationalize quorum-sensing triggered gene expression.
Authors: Rajasree, K. / Fasim, A. / Gopal, B.
History
DepositionFeb 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: DNA (5'-D(*TP*TP*TP*AP*AP*CP*AP*GP*TP*TP*AP*AP*GP*TP*AP*T)-3')
C: DNA (5'-D(*AP*AP*TP*AP*CP*TP*TP*AP*AP*CP*TP*GP*TP*TP*AP*A)-3')
A: Accessory gene regulator A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2114
Polymers22,1493
Non-polymers621
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-12 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.770, 47.770, 100.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: DNA chain DNA (5'-D(*TP*TP*TP*AP*AP*CP*AP*GP*TP*TP*AP*AP*GP*TP*AP*T)-3')


Mass: 4911.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*AP*AP*TP*AP*CP*TP*TP*AP*AP*CP*TP*GP*TP*TP*AP*A)-3')


Mass: 4880.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Accessory gene regulator A


Mass: 12357.919 Da / Num. of mol.: 1 / Fragment: LytTR domain (UNP RESIDUES 137-238)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: agrA, SACOL2026 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): RosettapLysS / References: UniProt: Q5HEG2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M Bis-Tris pH 6.0, 40% PEG 400.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.38→50.12 Å / Num. obs: 8820 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rsym value: 0.081 / Net I/σ(I): 9.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
SCALAdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.4→47.77 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.583 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.414 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23752 437 5 %RANDOM
Rwork0.20084 ---
obs0.2026 8347 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.988 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å2-0 Å2-0 Å2
2--1.8 Å2-0 Å2
3----3.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms865 650 4 22 1541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0151616
X-RAY DIFFRACTIONr_bond_other_d0.0040.021199
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.5662311
X-RAY DIFFRACTIONr_angle_other_deg1.30632777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3275104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94723.65452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17515165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.831158
X-RAY DIFFRACTIONr_chiral_restr0.0930.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021388
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02372
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1153.738413
X-RAY DIFFRACTIONr_mcbond_other3.0923.738412
X-RAY DIFFRACTIONr_mcangle_it4.635.589515
X-RAY DIFFRACTIONr_mcangle_other4.6295.59516
X-RAY DIFFRACTIONr_scbond_it4.4854.8311203
X-RAY DIFFRACTIONr_scbond_other4.4854.8311203
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6917.2121796
X-RAY DIFFRACTIONr_long_range_B_refined9.08342.5276645
X-RAY DIFFRACTIONr_long_range_B_other9.08342.5286646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 47 -
Rwork0.261 589 -
obs--100 %

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