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- PDB-5hs5: Crystal structure of Staphylococcus aureus SarX -

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Basic information

Entry
Database: PDB / ID: 5hs5
TitleCrystal structure of Staphylococcus aureus SarX
ComponentsHTH-type transcriptional regulator SarX
KeywordsTRANSCRIPTIONAL REGULATOR / Staphylococcus aureus / SarX / Virulence Regulator
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Transcriptional regulator SarA/Rot / : / Transcriptional regulator SarA/Rot / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
HTH-type transcriptional regulator SarX / HTH-type transcriptional regulator SarX
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsZhang, F. / Song, Y. / Li, X. / Teng, M.K.
Funding support China, 2items
OrganizationGrant numberCountry
the Chinese Ministry of Science and Technology2012CB917200 and 2009CB825500 China
the Chinese National Natural Science Foundation31270014, 31130018, 30900224 and 10979039 China
CitationJournal: To Be Published
Title: Crystal structure of Staphylococcus aureus SarX
Authors: Zhang, F. / Song, Y. / Li, X. / Teng, M.K.
History
DepositionJan 25, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: HTH-type transcriptional regulator SarX
B: HTH-type transcriptional regulator SarX


Theoretical massNumber of molelcules
Total (without water)29,3912
Polymers29,3912
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-19 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.170, 56.170, 153.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein HTH-type transcriptional regulator SarX / Staphylococcal accessory regulator X


Mass: 14695.537 Da / Num. of mol.: 2 / Fragment: UNP residues 7-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300 (bacteria)
Strain: USA300 / Gene: sarX, SAUSA300_0654 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FIX1, UniProt: Q2G0D1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.01 M Iron (III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate,10%(v/v) Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 9620 / % possible obs: 99.2 % / Redundancy: 15.1 % / Net I/σ(I): 19.7
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 5.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
Cootmodel building
PHENIXphasing
iMOSFLMdata processing
RefinementMethod to determine structure: SAD / Resolution: 2.55→46.4 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / ESU R: 0.618 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28118 545 5.7 %RANDOM
Rwork0.22822 ---
obs0.23121 9038 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.787 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.65 Å2-0 Å2
2--0.65 Å2-0 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.55→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 0 16 1834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191842
X-RAY DIFFRACTIONr_bond_other_d00.021763
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9952485
X-RAY DIFFRACTIONr_angle_other_deg3.70334022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0075230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75324.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48915321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.781158
X-RAY DIFFRACTIONr_chiral_restr0.0810.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022056
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02408
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_it3.7525.172926
X-RAY DIFFRACTIONr_mcbond_other3.7455.17925
X-RAY DIFFRACTIONr_mcangle_it5.6947.7481154
X-RAY DIFFRACTIONr_mcangle_other5.6937.7511155
X-RAY DIFFRACTIONr_scbond_it4.5055.48915
X-RAY DIFFRACTIONr_scbond_other4.5035.482916
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1858.0661331
X-RAY DIFFRACTIONr_long_range_B_refined9.06639.9262052
X-RAY DIFFRACTIONr_long_range_B_other9.06739.9312050
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 41 -
Rwork0.336 617 -
obs--99.4 %

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