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- PDB-7jl6: Heme binding to SrrB PAS domain plays a role in redox regulation ... -

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Basic information

Entry
Database: PDB / ID: 7jl6
TitleHeme binding to SrrB PAS domain plays a role in redox regulation of S. aureus SrrAB two-component system
ComponentsSensor protein SrrB
KeywordsMEMBRANE PROTEIN / metal binding protein
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / ATP binding / plasma membrane
Similarity search - Function
ResE, histidine kinase sensor domain / Histidine kinase sensor domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily ...ResE, histidine kinase sensor domain / Histidine kinase sensor domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.1 Å
AuthorsTiwari, N. / Sun, Y.J. / Gakhar, L. / Fuentes, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI135305 United States
CitationJournal: To Be Published
Title: Heme binding to SrrB PAS domain plays a role in redox regulation of S. aureus SrrAB two-component system
Authors: Tiwari, N. / Sun, Y.J. / Fuentes, E.J.
History
DepositionJul 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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: Sensor protein SrrB
B: Sensor protein SrrB


Theoretical massNumber of molelcules
Total (without water)23,6592
Polymers23,6592
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-12 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.072, 65.140, 37.513
Angle α, β, γ (deg.)90.00, 91.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sensor protein SrrB / Staphylococcal respiratory response protein B


Mass: 11829.364 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: srrB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9L523, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4M sodium malonate pH 7.0 / PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jan 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.1→51.49 Å / Num. obs: 10615 / % possible obs: 94 % / Redundancy: 10.8 % / Biso Wilson estimate: 25.18 Å2 / Rrim(I) all: 0.2348 / Net I/σ(I): 3.28
Reflection shellResolution: 2.1→51.49 Å / Num. unique obs: 1041 / Rrim(I) all: 0.2348 / % possible all: 94.13

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.1→51.49 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.369 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23437 592 5.3 %RANDOM
Rwork0.19211 ---
obs0.19444 10615 94.2 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.401 Å2
Baniso -1Baniso -2Baniso -3
1-4.99 Å20 Å20.4 Å2
2---1.64 Å2-0 Å2
3----3.36 Å2
Refinement stepCycle: LAST / Resolution: 2.1→51.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 0 27 1562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191544
X-RAY DIFFRACTIONr_bond_other_d0.0010.021464
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.9022069
X-RAY DIFFRACTIONr_angle_other_deg1.0152.9343401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.855192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06125.76978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6715314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7481511
X-RAY DIFFRACTIONr_chiral_restr0.0770.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02286
X-RAY DIFFRACTIONr_mcbond_it3.6023.099774
X-RAY DIFFRACTIONr_mcbond_other3.5853.095773
X-RAY DIFFRACTIONr_mcangle_it5.1124.629964
X-RAY DIFFRACTIONr_mcangle_other5.114.634965
X-RAY DIFFRACTIONr_scbond_it4.4623.636770
X-RAY DIFFRACTIONr_scbond_other4.4593.64771
X-RAY DIFFRACTIONr_scangle_other6.5365.2411106
X-RAY DIFFRACTIONr_long_range_B_refined8.436.6541615
X-RAY DIFFRACTIONr_long_range_B_other8.40136.6911614
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 34 -
Rwork0.258 720 -
obs--86.77 %

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