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

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Basic information

Entry
Database: PDB / ID: 4xxe
TitleStructure of AgrA LytTR domain in complex with promoters
Components
  • Accessory gene regulator A
  • DNA (5'-D(*AP*TP*TP*GP*CP*CP*TP*AP*AP*CP*TP*GP*TP*AP*G)-3')
  • DNA (5'-D(P*TP*AP*CP*AP*GP*TP*TP*AP*GP*GP*CP*AP*A)-3')
  • DNA (5'-D(P*TP*AP*CP*AP*GP*TP*TP*AP*GP*GP*CP*AP*T)-3')
KeywordsTRANSCRIPTION/DNA / Protein-DNA complex / TRANSCRIPTION-DNA 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 / SYNCHROTRON / Resolution: 3.2 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
DepositionJan 30, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Accessory gene regulator A
B: DNA (5'-D(P*TP*AP*CP*AP*GP*TP*TP*AP*GP*GP*CP*AP*A)-3')
C: DNA (5'-D(*AP*TP*TP*GP*CP*CP*TP*AP*AP*CP*TP*GP*TP*AP*G)-3')
D: Accessory gene regulator A
E: DNA (5'-D(P*TP*AP*CP*AP*GP*TP*TP*AP*GP*GP*CP*AP*T)-3')
F: DNA (5'-D(*AP*TP*TP*GP*CP*CP*TP*AP*AP*CP*TP*GP*TP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)40,9796
Polymers40,9796
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-43 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.760, 96.760, 51.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALILEILEAA140 - 2381 - 99
21VALVALILEILEDD140 - 2381 - 99
12DTDTDADABB4 - 161 - 13
22DTDTDTDTEE4 - 161 - 13
13DADADGDGCC1 - 151 - 15
23DADADGDGFF1 - 151 - 15

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Accessory gene regulator A


Mass: 11910.455 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 140-238
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
#2: DNA chain DNA (5'-D(P*TP*AP*CP*AP*GP*TP*TP*AP*GP*GP*CP*AP*A)-3')


Mass: 3999.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*TP*TP*GP*CP*CP*TP*AP*AP*CP*TP*GP*TP*AP*G)-3')


Mass: 4583.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*TP*AP*CP*AP*GP*TP*TP*AP*GP*GP*CP*AP*T)-3')


Mass: 3990.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6% Tacsimate pH 7.0 0.1M MES monohydrate pH 6.0 25% PEG4000 0.1M CoCl2 hexahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 3.2→97.03 Å / Num. obs: 8048 / % possible obs: 100 % / Redundancy: 8.1 % / Rsym value: 0.127 / Net I/σ(I): 8.6
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALAdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 3.2→96.76 Å / Cor.coef. Fo:Fc: 0.812 / Cor.coef. Fo:Fc free: 0.873 / SU B: 58.993 / SU ML: 0.931 / Cross valid method: THROUGHOUT / ESU R Free: 0.722 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35517 759 9.5 %RANDOM
Rwork0.31477 ---
obs0.3187 7228 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 131.789 Å2
Baniso -1Baniso -2Baniso -3
1--2.95 Å2-0 Å2-0 Å2
2---2.95 Å2-0 Å2
3---5.9 Å2
Refinement stepCycle: LAST / Resolution: 3.2→96.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 1145 0 0 2726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0152893
X-RAY DIFFRACTIONr_bond_other_d0.0030.022071
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.5664144
X-RAY DIFFRACTIONr_angle_other_deg1.64134777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7855196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53923.63688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65715265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.611512
X-RAY DIFFRACTIONr_chiral_restr0.1140.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022547
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02690
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_it10.22612.619790
X-RAY DIFFRACTIONr_mcbond_other10.21512.616789
X-RAY DIFFRACTIONr_mcangle_it15.6918.876984
X-RAY DIFFRACTIONr_mcangle_other15.68518.882985
X-RAY DIFFRACTIONr_scbond_it11.47914.3522103
X-RAY DIFFRACTIONr_scbond_other11.47514.352102
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other18.22921.5153159
X-RAY DIFFRACTIONr_long_range_B_refined26.62611854
X-RAY DIFFRACTIONr_long_range_B_other26.62611855
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A110580.03
12D110580.03
21B19720.05
22E19720.05
31C23400.01
32F23400.01
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.518 58 -
Rwork0.457 501 -
obs--100 %

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