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

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Basic information

Entry
Database: PDB / ID: 4xqq
TitleCrystal structure of AgrA LytTR domain in complex with promoters
Components
  • Accessory gene regulator A
  • DNA (5'-D(*AP*TP*TP*TP*CP*TP*TP*AP*AP*CP*TP*AP*GP*TP*CP*G)-3')
  • DNA (5'-D(*TP*CP*GP*AP*CP*TP*AP*GP*TP*TP*AP*AP*GP*AP*AP*A)-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
DNA / DNA (> 10) / Accessory gene regulator A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.05 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 27, 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 1.2Dec 25, 2019Group: Derived calculations
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn
Revision 1.3Mar 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: Accessory gene regulator A
C: Accessory gene regulator A
D: Accessory gene regulator A
E: DNA (5'-D(*TP*CP*GP*AP*CP*TP*AP*GP*TP*TP*AP*AP*GP*AP*AP*A)-3')
F: DNA (5'-D(*AP*TP*TP*TP*CP*TP*TP*AP*AP*CP*TP*AP*GP*TP*CP*G)-3')
G: DNA (5'-D(*TP*CP*GP*AP*CP*TP*AP*GP*TP*TP*AP*AP*GP*AP*AP*A)-3')
H: DNA (5'-D(*AP*TP*TP*TP*CP*TP*TP*AP*AP*CP*TP*AP*GP*TP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)67,5778
Polymers67,5778
Non-polymers00
Water00
1
G: DNA (5'-D(*TP*CP*GP*AP*CP*TP*AP*GP*TP*TP*AP*AP*GP*AP*AP*A)-3')
H: DNA (5'-D(*AP*TP*TP*TP*CP*TP*TP*AP*AP*CP*TP*AP*GP*TP*CP*G)-3')

A: Accessory gene regulator A

D: Accessory gene regulator A


Theoretical massNumber of molelcules
Total (without water)33,7884
Polymers33,7884
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_456-x-1/2,y+1/2,-z+11
2
B: Accessory gene regulator A
C: Accessory gene regulator A
E: DNA (5'-D(*TP*CP*GP*AP*CP*TP*AP*GP*TP*TP*AP*AP*GP*AP*AP*A)-3')
F: DNA (5'-D(*AP*TP*TP*TP*CP*TP*TP*AP*AP*CP*TP*AP*GP*TP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)33,7884
Polymers33,7884
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.020, 145.600, 62.100
Angle α, β, γ (deg.)90.00, 93.09, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27G
18F
28H

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
11GLUGLULYSLYSAA141 - 2373 - 99
21GLUGLULYSLYSBB141 - 2373 - 99
12VALVALILEILEAA140 - 2382 - 100
22VALVALILEILECC140 - 2382 - 100
13VALVALLYSLYSAA140 - 2372 - 99
23VALVALLYSLYSDD140 - 2372 - 99
14GLUGLULYSLYSBB141 - 2373 - 99
24GLUGLULYSLYSCC141 - 2373 - 99
15GLUGLULYSLYSBB141 - 2373 - 99
25GLUGLULYSLYSDD141 - 2373 - 99
16VALVALLYSLYSCC140 - 2372 - 99
26VALVALLYSLYSDD140 - 2372 - 99
17DTDTDADAEE1 - 161 - 16
27DTDTDADAGG1 - 161 - 16
18DADADGDGFF1 - 161 - 16
28DADADGDGHH1 - 161 - 16

NCS ensembles :
ID
1
2
3
4
5
6
7
8

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Components

#1: Protein
Accessory gene regulator A


Mass: 11997.532 Da / Num. of mol.: 4 / Fragment: LytTR domain (UNP RESIDUES 139-238)
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
#2: DNA chain DNA (5'-D(*TP*CP*GP*AP*CP*TP*AP*GP*TP*TP*AP*AP*GP*AP*AP*A)-3')


Mass: 4930.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*TP*TP*TP*CP*TP*TP*AP*AP*CP*TP*AP*GP*TP*CP*G)-3')


Mass: 4863.176 Da / Num. of mol.: 2 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6% Tacsimate, 0.1M MES monohydrate pH 6.0, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.05→62.01 Å / Num. obs: 13297 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rsym value: 0.096 / Net I/σ(I): 6.9
Reflection shellResolution: 3.05→3.26 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.34 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
SCALAdata reduction
SCALAdata scaling
PHENIXphasing
RefinementResolution: 3.05→62.01 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.916 / SU B: 40.251 / SU ML: 0.65 / Cross valid method: THROUGHOUT / ESU R Free: 0.565 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30501 654 4.9 %RANDOM
Rwork0.26139 ---
obs0.26347 12641 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 113.393 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å2-0 Å2-10.52 Å2
2---0.05 Å20 Å2
3---2.92 Å2
Refinement stepCycle: LAST / Resolution: 3.05→62.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3186 1300 0 0 4486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0174704
X-RAY DIFFRACTIONr_bond_other_d0.0080.023674
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.6696623
X-RAY DIFFRACTIONr_angle_other_deg1.81338409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0145392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08423.034178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70115534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7351529
X-RAY DIFFRACTIONr_chiral_restr0.0830.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024527
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021166
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_it4.78311.3961580
X-RAY DIFFRACTIONr_mcbond_other4.78211.3931579
X-RAY DIFFRACTIONr_mcangle_it7.79417.0891968
X-RAY DIFFRACTIONr_mcangle_other7.79317.0921969
X-RAY DIFFRACTIONr_scbond_it4.74512.1153123
X-RAY DIFFRACTIONr_scbond_other4.74412.1153122
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.83718.1544655
X-RAY DIFFRACTIONr_long_range_B_refined13.82619544
X-RAY DIFFRACTIONr_long_range_B_other13.82619545
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)
11A111420.09
12B111420.09
21A106500.12
22C106500.12
31A101700.11
32D101700.11
41B100080.11
42C100080.11
51B99800.09
52D99800.09
61C95440.11
62D95440.11
71E24820.08
72G24820.08
81F27140.03
82H27140.03
LS refinement shellResolution: 3.05→3.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 50 -
Rwork0.409 934 -
obs--99.19 %

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