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- PDB-6e52: Chimeric structure of Saccharomyces cerevisiae GCN4 leucine zippe... -

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Basic information

Entry
Database: PDB / ID: 6.0E+52
TitleChimeric structure of Saccharomyces cerevisiae GCN4 leucine zipper fused to Staphylococcus aureus AgrC cytoplasmic histidine kinase module (dataset anisotropically truncated by STARANISO)
ComponentsStaphylococcus aureus AgrC histidine kinase module fused to Saccharomyces cerevisiae GCN4 leucine zipper
KeywordsSIGNALING PROTEIN / Protein histidine kinase / bacterial quorum sensing / coiled coil / Bergerat fold
Function / homology
Function and homology information


Activation of the AP-1 family of transcription factors / protein localization to nuclear periphery / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / response to amino acid starvation / mediator complex binding / amino acid biosynthetic process / TFIID-class transcription factor complex binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II ...Activation of the AP-1 family of transcription factors / protein localization to nuclear periphery / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / response to amino acid starvation / mediator complex binding / amino acid biosynthetic process / TFIID-class transcription factor complex binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / kinase activity / transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / identical protein binding / nucleus
Similarity search - Function
Sensor histidine kinase NatK, C-terminal domain / GHKL domain / : / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Accessory gene regulator C (Histidine kinase) / General control transcription factor GCN4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Staphylococcus aureus subsp. aureus Z172 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsXie, Q. / Jeffrey, P.D. / Muir, T.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI042783 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095880 United States
CitationJournal: Cell Chem Biol / Year: 2019
Title: Identification of a Molecular Latch that Regulates Staphylococcal Virulence.
Authors: Xie, Q. / Zhao, A. / Jeffrey, P.D. / Kim, M.K. / Bassler, B.L. / Stone, H.A. / Novick, R.P. / Muir, T.W.
History
DepositionJul 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Staphylococcus aureus AgrC histidine kinase module fused to Saccharomyces cerevisiae GCN4 leucine zipper
B: Staphylococcus aureus AgrC histidine kinase module fused to Saccharomyces cerevisiae GCN4 leucine zipper


Theoretical massNumber of molelcules
Total (without water)57,6882
Polymers57,6882
Non-polymers00
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-45 kcal/mol
Surface area26340 Å2
MethodPISA
2
A: Staphylococcus aureus AgrC histidine kinase module fused to Saccharomyces cerevisiae GCN4 leucine zipper
B: Staphylococcus aureus AgrC histidine kinase module fused to Saccharomyces cerevisiae GCN4 leucine zipper

A: Staphylococcus aureus AgrC histidine kinase module fused to Saccharomyces cerevisiae GCN4 leucine zipper
B: Staphylococcus aureus AgrC histidine kinase module fused to Saccharomyces cerevisiae GCN4 leucine zipper


Theoretical massNumber of molelcules
Total (without water)115,3754
Polymers115,3754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area16190 Å2
ΔGint-108 kcal/mol
Surface area49070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.141, 83.375, 146.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-439-

HOH

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Components

#1: Protein Staphylococcus aureus AgrC histidine kinase module fused to Saccharomyces cerevisiae GCN4 leucine zipper / Amino acid biosynthesis regulatory protein


Mass: 28843.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Chimera constructed by fusing Saccharomyces cerevisiae GCN4 leucine zipper (residues 250-274) to the N-terminus of Staphylococcus aureus AgrC cytoplasmic histidine kinase module (residues 209-430)
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Staphylococcus aureus subsp. aureus Z172 (bacteria)
Strain: ATCC 204508 / S288c / Gene: GCN4, AAS3, ARG9, YEL009C, agrC, SAZ172_2038 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03069, UniProt: A0A0E1AMS6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 3.36 Å3/Da / Density % sol: 63.34 % / Description: Plate-shaped crystal
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris pH 8.0 and 2.8 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.93→31.76 Å / Num. obs: 36936 / % possible obs: 61.6 % / Redundancy: 6.4 % / CC1/2: 0.99 / Rpim(I) all: 0.035 / Rrim(I) all: 0.087 / Rsym value: 0.08 / Χ2: 1.01 / Net I/σ(I): 11.9
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 312 / CC1/2: 0.49 / Rpim(I) all: 0.655 / Rrim(I) all: 1.405 / Rsym value: 1.236 / Χ2: 1.05 / % possible all: 7.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.93→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.581 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.21 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26807 1830 5 %RANDOM
Rwork0.21839 ---
obs0.22081 35104 62.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.216 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å20 Å2
2--0.43 Å20 Å2
3----1.77 Å2
Refinement stepCycle: 1 / Resolution: 1.93→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3813 0 0 250 4063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133886
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173696
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.6375243
X-RAY DIFFRACTIONr_angle_other_deg1.3211.5788613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.015476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06724.395223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86215772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1551522
X-RAY DIFFRACTIONr_chiral_restr0.0720.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02716
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_it3.7464.9061892
X-RAY DIFFRACTIONr_mcbond_other3.7464.9041891
X-RAY DIFFRACTIONr_mcangle_it5.5217.3332360
X-RAY DIFFRACTIONr_mcangle_other5.527.3362361
X-RAY DIFFRACTIONr_scbond_it4.255.2591994
X-RAY DIFFRACTIONr_scbond_other4.2495.2611995
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5137.722879
X-RAY DIFFRACTIONr_long_range_B_refined9.62457.6774529
X-RAY DIFFRACTIONr_long_range_B_other9.52157.4844465
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 15 -
Rwork0.309 336 -
obs--8.11 %

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