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- PDB-3hrm: Crystal structure of Staphylococcus aureus protein SarZ in sulfen... -

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Basic information

Entry
Database: PDB / ID: 3hrm
TitleCrystal structure of Staphylococcus aureus protein SarZ in sulfenic acid form
ComponentsHTH-type transcriptional regulator sarZ
KeywordsTRANSCRIPTION REGULATOR / helix-turn-helix / cysteine sulfenic acid / 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 / SAD / Resolution: 2.3 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 9, 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.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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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)33,0412
Polymers33,0412
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-45 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.400, 54.030, 113.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HTH-type transcriptional regulator sarZ


Mass: 16520.697 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.: 39 / 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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 0.1 M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97935 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.3→35.42 Å / Num. obs: 12976 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.082 / Χ2: 1.735 / Net I/σ(I): 31.722
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.732 / Num. unique all: 1261 / Χ2: 1.022 / % possible all: 99.7

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.5070.6870.1841.359
2Se600.0820.0890.0951.275
3Se600.4930.5770.130.808
4Se600.2210.9780.0810.823

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.3→35.42 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.786 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.286 636 4.9 %Random
Rwork0.238 ---
obs-12928 99.9 %-
Solvent computationBsol: 41.758 Å2
Displacement parametersBiso max: 103.21 Å2 / Biso mean: 49.457 Å2 / Biso min: 20.41 Å2
Baniso -1Baniso -2Baniso -3
1-1.415 Å20 Å20 Å2
2---0.767 Å20 Å2
3----0.648 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 0 39 2210
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.095
LS refinement shellResolution: 2.3→2.38 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_repCSO.param
X-RAY DIFFRACTION2water_rep.param

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