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- PDB-3hse: Crystal structure of Staphylococcus aureus protein SarZ in reduce... -

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Basic information

Entry
Database: PDB / ID: 3hse
TitleCrystal structure of Staphylococcus aureus protein SarZ in reduced form
ComponentsHTH-type transcriptional regulator sarZ
KeywordsTRANSCRIPTION REGULATOR / helix-turn-helix / MarR-family transcriptional regulator / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
MarR family regulatory protein / MarR family regulatory protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsPoor, C.B. / Duguid, E. / Rice, P.A. / He, C.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structures of the reduced, sulfenic acid, and mixed disulfide forms of SarZ, a redox active global regulator in Staphylococcus aureus.
Authors: Poor, C.B. / Chen, P.R. / Duguid, E. / Rice, P.A. / He, C.
History
DepositionJun 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator sarZ
B: HTH-type transcriptional regulator sarZ


Theoretical massNumber of molelcules
Total (without water)32,8222
Polymers32,8222
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-49.1 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.830, 60.830, 192.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-145-

HOH

DetailsThe biological assembly is the dimer found in the asymmetric unit.

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Components

#1: Protein HTH-type transcriptional regulator sarZ


Mass: 16410.908 Da / Num. of mol.: 2 / Fragment: UNP residues 7-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Newman / Gene: NWMN_2286 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6QJM6, UniProt: A0A0H3KA72*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 3.2 M ammonium sulfate, 0.1 M citric acid , pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97857 Å
DetectorType: SBC-3 / Detector: CCD / Date: Feb 6, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.9→28.71 Å / Num. obs: 8051 / Redundancy: 5.6 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 25.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.496

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å23.88 Å
Translation4 Å23.88 Å

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Processing

Software
NameVersionClassificationNB
PHASER1.3.2phasing
CNSrefinement
PDB_EXTRACT3.005data extraction
SBC-CollectSBCCOLLECTdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HRM

3hrm


Resolution: 2.9→28.71 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.722 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.317 468 4.4 %Random
Rwork0.286 ---
obs-7721 89.4 %-
Solvent computationBsol: 63.289 Å2
Displacement parametersBiso max: 122.22 Å2 / Biso mean: 77.593 Å2 / Biso min: 39.28 Å2
Baniso -1Baniso -2Baniso -3
1--8.028 Å20 Å20 Å2
2---8.028 Å20 Å2
3---16.056 Å2
Refinement stepCycle: LAST / Resolution: 2.9→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 0 10 1943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.299
LS refinement shellResolution: 2.9→3 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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