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- PDB-3bs1: Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to... -

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Basic information

Entry
Database: PDB / ID: 3bs1
TitleStructure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with a Novel Mode of Binding
Components
  • Accessory gene regulator protein A
  • DNA (5'-D(*DAP*DAP*(BRU)P*DAP*DCP*DTP*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DTP*DAP*DA)-3')
  • DNA (5'-D(*DTP*DTP*DTP*DAP*DAP*DCP*DAP*DGP*DTP*DTP*DAP*DAP*DGP*(BRU)P*DAP*DT)-3')
Keywordstranscription regulator / LytTR / AgrA / response regulator / DNA binding domain / Activator / Cytoplasm / DNA-binding / Phosphoprotein / Transcription / Transcription regulation / Two-component regulatory system
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 protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsSidote, D.J. / Barbieri, C. / Wu, T. / Stock, A.M.
CitationJournal: Structure / Year: 2008
Title: Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with an Unusual Mode of Binding.
Authors: Sidote, D.J. / Barbieri, C.M. / Wu, T. / Stock, A.M.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*DTP*DTP*DTP*DAP*DAP*DCP*DAP*DGP*DTP*DTP*DAP*DAP*DGP*(BRU)P*DAP*DT)-3')
C: DNA (5'-D(*DAP*DAP*(BRU)P*DAP*DCP*DTP*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DTP*DAP*DA)-3')
A: Accessory gene regulator protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3285
Polymers22,2793
Non-polymers492
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-12.5 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.938, 47.938, 100.112
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(*DTP*DTP*DTP*DAP*DAP*DCP*DAP*DGP*DTP*DTP*DAP*DAP*DGP*(BRU)P*DAP*DT)-3')


Mass: 4976.097 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Staphylococcus aureus
#2: DNA chain DNA (5'-D(*DAP*DAP*(BRU)P*DAP*DCP*DTP*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DTP*DAP*DA)-3')


Mass: 4945.086 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Staphylococcus aureus
#3: Protein Accessory gene regulator protein A


Mass: 12357.919 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 137-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: DB / Gene: agrA, agr / Plasmid: pET9a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A0I7
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 40% PEG 400, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2Bis-TrisBis-tris methane11
3PEG 40012
4Bis-TrisBis-tris methane12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9204 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9204 Å / Relative weight: 1
ReflectionResolution: 1.6→17.3 Å / Num. all: 29714 / Num. obs: 29714 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18.4 Å2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 5.7 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→17.3 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.717 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.091
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22066 1485 5.1 %RANDOM
Rwork0.19534 ---
all0.1961 29714 --
obs0.19659 27747 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.945 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→17.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms872 650 2 223 1747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211617
X-RAY DIFFRACTIONr_angle_refined_deg1.3812.4452313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9985104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56423.65452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.46115169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.397158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021019
X-RAY DIFFRACTIONr_nbd_refined0.1870.2583
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21021
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3740.2189
X-RAY DIFFRACTIONr_metal_ion_refined0.0230.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.234
X-RAY DIFFRACTIONr_mcbond_it0.7681.5532
X-RAY DIFFRACTIONr_mcangle_it1.2162839
X-RAY DIFFRACTIONr_scbond_it1.36431440
X-RAY DIFFRACTIONr_scangle_it1.9964.51473
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 112 -
Rwork0.213 1983 -
obs--97.26 %

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