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- PDB-4xqj: Crystal structure of AgrA LytTR domain in complex with promoters -

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Basic information

Entry
Database: PDB / ID: 4xqj
TitleCrystal structure of AgrA LytTR domain in complex with promoters
Components
  • Accessory gene regulator A
  • DNA (5'-D(*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
  • DNA (5'-D(P*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / DNA BINDING PROTEIN-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
ETHANOL / DNA / DNA (> 10) / Accessory gene regulator A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 19, 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_symmetry / _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*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
C: DNA (5'-D(*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
D: Accessory gene regulator A
E: DNA (5'-D(P*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
F: DNA (5'-D(*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,37531
Polymers39,0916
Non-polymers1,28425
Water2,990166
1
A: Accessory gene regulator A
B: DNA (5'-D(P*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
C: DNA (5'-D(*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,16215
Polymers19,5463
Non-polymers61712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Accessory gene regulator A
E: DNA (5'-D(P*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
F: DNA (5'-D(*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,21216
Polymers19,5463
Non-polymers66713
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.030, 92.870, 45.150
Angle α, β, γ (deg.)90.00, 98.59, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12C
22F

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
11VALVALLYSLYSAA140 - 2361 - 97
21VALVALLYSLYSDD140 - 2361 - 97
12DADADTDTCC1 - 131 - 13
22DADADTDTFF1 - 131 - 13

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Accessory gene regulator A


Mass: 11910.455 Da / Num. of mol.: 2 / Fragment: LytTR domain (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): Rosetta(DE3)pLysS / References: UniProt: Q5HEG2

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DNA chain , 2 types, 4 molecules BECF

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


Mass: 3694.455 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')


Mass: 3940.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 191 molecules

#4: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.05M Calcium chloride dihydrate 0.1M MES monohydrate pH 6.0 45% PEG 200

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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 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.9→35.02 Å / Num. obs: 29281 / % possible obs: 100 % / Redundancy: 4.4 % / Rsym value: 0.065 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALAdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BS1

3bs1


Resolution: 1.9→35.02 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.731 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22475 1422 4.9 %RANDOM
Rwork0.18757 ---
obs0.18931 27856 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.663 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å2-0 Å21.48 Å2
2---0.58 Å2-0 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1645 999 80 166 2890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0162858
X-RAY DIFFRACTIONr_bond_other_d0.0050.022237
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.6124018
X-RAY DIFFRACTIONr_angle_other_deg1.39635133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9995199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15823.4100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33515300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4661516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022518
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02673
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_it2.3163.177790
X-RAY DIFFRACTIONr_mcbond_other2.3023.173789
X-RAY DIFFRACTIONr_mcangle_it3.4564.738985
X-RAY DIFFRACTIONr_mcangle_other3.4554.742986
X-RAY DIFFRACTIONr_scbond_it3.2754.4392068
X-RAY DIFFRACTIONr_scbond_other3.2684.4392068
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.116.6273032
X-RAY DIFFRACTIONr_long_range_B_refined8.66137.96411858
X-RAY DIFFRACTIONr_long_range_B_other8.6637.96411859
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)
11A116000.1
12D116000.1
21C20660.09
22F20660.09
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 116 -
Rwork0.291 2054 -
obs--99.91 %

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