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- PDB-6m8o: Crystal structure of the receiver domain of LytR from Staphylococ... -

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Basic information

Entry
Database: PDB / ID: 6m8o
TitleCrystal structure of the receiver domain of LytR from Staphylococcus aureus
ComponentsDNA-binding response regulator
KeywordsSIGNALING PROTEIN / Two-Component System / Response Regulator / Receiver Domain
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
: / 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 ...: / 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 / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulatory protein LytR / Autolysis response regulater LytR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShala-Lawrence, A. / Audette, G.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-06218-2014 Canada
Citation
Journal: To Be Published
Title: Crystal structure of the receiver domain of LytR from Staphylococcus aureus
Authors: Shala-Lawrence, A. / Audette, G.F.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Expression, purification, crystallization and preliminary X-ray analysis of the receiver domain of Staphylococcus aureus LytR protein.
Authors: Shala, A. / Patel, K.H. / Golemi-Kotra, D. / Audette, G.F.
History
DepositionAug 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: DNA-binding response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1382
Polymers15,0421
Non-polymers961
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA-binding response regulator
hetero molecules

A: DNA-binding response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2764
Polymers30,0842
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area1580 Å2
ΔGint-34 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.747, 84.747, 157.304
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein DNA-binding response regulator / Sensory transduction protein LytR / Two-component response regulator


Mass: 15041.998 Da / Num. of mol.: 1 / Fragment: Response regulatory domain, residues 1-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: C3B39_09020, EP54_06415, EQ90_12235, HMPREF3211_02791 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: W8UTS7, UniProt: P60611*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 5.44 Å3/Da / Density % sol: 77.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES (pH 6.5), 1.6 M magnesium sulfate heptahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→42.66 Å / Num. obs: 12211 / % possible obs: 99.9 % / Redundancy: 20.9 % / Biso Wilson estimate: 80.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.026 / Rrim(I) all: 0.089 / Χ2: 0.98 / Net I/σ(I): 20.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 21.5 % / Rmerge(I) obs: 2.607 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1323 / CC1/2: 0.91 / Rpim(I) all: 0.781 / Rrim(I) all: 2.669 / Χ2: 0.93 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qvo

2qvo


Resolution: 2.5→42.7 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 18.513 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23666 628 5.2 %RANDOM
Rwork0.19944 ---
obs0.20136 11533 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.566 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å21.03 Å2-0 Å2
2--2.05 Å20 Å2
3----6.66 Å2
Refinement stepCycle: 1 / Resolution: 2.5→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 5 13 948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.014947
X-RAY DIFFRACTIONr_bond_other_d0.0010.017878
X-RAY DIFFRACTIONr_angle_refined_deg2.3061.6541282
X-RAY DIFFRACTIONr_angle_other_deg1.2781.6342052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4665117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98626.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.89515171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.048152
X-RAY DIFFRACTIONr_chiral_restr0.1130.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021050
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02158
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_it5.396.565471
X-RAY DIFFRACTIONr_mcbond_other5.2536.562470
X-RAY DIFFRACTIONr_mcangle_it7.3969.832587
X-RAY DIFFRACTIONr_mcangle_other7.3929.84588
X-RAY DIFFRACTIONr_scbond_it6.4077.142475
X-RAY DIFFRACTIONr_scbond_other5.9717.126471
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.38610.443689
X-RAY DIFFRACTIONr_long_range_B_refined9.10278.2771048
X-RAY DIFFRACTIONr_long_range_B_other9.10778.3451049
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 41 -
Rwork0.373 834 -
obs--99.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.68031.4960.32211.4641.76295.85790.0594-0.2108-0.0663-0.1584-0.06280.2130.27620.05670.00330.30450.1214-0.02910.08980.00350.0118-4.351558.45922.0833
25.5205-2.3578-5.84236.77363.28177.17260.3809-0.5539-0.10860.0391-0.1061-0.1371-0.15430.5098-0.27480.31840.054-0.05330.22610.05790.2255-2.075353.789110.2062
31.00271.1562-0.016111.43841.63946.2887-0.04980.43510.0456-0.76710.0751-0.04110.32060.2219-0.02530.32560.05680.01720.22510.02160.0257-2.231360.1599-7.1658
46.70832.02523.58874.1988-1.37647.823-0.0391-0.44960.1866-0.0033-0.1360.2506-0.2062-0.39510.17510.28590.0786-0.00220.2141-0.0610.166-6.295565.53249.596
5355.375442.2811-73.529254.2541-18.4443411.5566-0.6256-1.0256-4.1826-0.98862.91531.2083-3.37512.3084-2.28970.46750.03620.04990.4392-0.00990.470110.283856.39520.7606
60.05760.0088-0.60871.12341.44918.64330.02250.0033-0.0070.39130.0697-0.16640.26210.1287-0.09210.21740.1115-0.04930.1146-0.02440.1275-3.780661.8737-0.1551
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 8
2X-RAY DIFFRACTION1A26 - 33
3X-RAY DIFFRACTION1A48 - 53
4X-RAY DIFFRACTION1A76 - 81
5X-RAY DIFFRACTION1A96 - 101
6X-RAY DIFFRACTION2A9 - 25
7X-RAY DIFFRACTION3A34 - 47
8X-RAY DIFFRACTION3A54 - 75
9X-RAY DIFFRACTION3A82 - 95
10X-RAY DIFFRACTION4A102 - 118
11X-RAY DIFFRACTION5A201
12X-RAY DIFFRACTION6A301 - 313

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