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- PDB-4gxo: Crystal structure of Staphylococcus aureus protein SarZ mutant C13E -

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Basic information

Entry
Database: PDB / ID: 4gxo
TitleCrystal structure of Staphylococcus aureus protein SarZ mutant C13E
ComponentsMarR family regulatory protein
KeywordsTRANSCRIPTION / transcriptional regulator / Structural Genomics
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSun, F. / Ding, Y. / Ji, Q. / Liang, Z. / Deng, X. / Wong, C.C. / Yi, C. / Zhang, L. / Xie, S. / Alvarez, S. ...Sun, F. / Ding, Y. / Ji, Q. / Liang, Z. / Deng, X. / Wong, C.C. / Yi, C. / Zhang, L. / Xie, S. / Alvarez, S. / Hicks, L.M. / Luo, C. / Jiang, H. / Lan, L. / He, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Protein cysteine phosphorylation of SarA/MgrA family transcriptional regulators mediates bacterial virulence and antibiotic resistance.
Authors: Sun, F. / Ding, Y. / Ji, Q. / Liang, Z. / Deng, X. / Wong, C.C. / Yi, C. / Zhang, L. / Xie, S. / Alvarez, S. / Hicks, L.M. / Luo, C. / Jiang, H. / Lan, L. / He, C.
History
DepositionSep 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MarR family regulatory protein
B: MarR family regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1505
Polymers32,8742
Non-polymers2763
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-40 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.442, 55.792, 119.260
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 MarR family regulatory protein


Mass: 16436.879 Da / Num. of mol.: 2 / Mutation: C13E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Newman / Gene: NWMN_2286, sarZ / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6QJM6, UniProt: A0A0H3KA72*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1 M Bis-Tris, 25% polyethylene glycol 3,350, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0782 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 19781 / Num. obs: 18598 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.05-2.12197.6
2.12-2.21199.6
2.21-2.311100
2.31-2.431100
2.43-2.581100
2.58-2.781100
2.78-3.061100
3.06-3.5199.9
3.5-4.41100
4.4-20199.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
X-PLORmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→19.88 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.132 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2702 1005 5.1 %RANDOM
Rwork0.2219 ---
obs0.22438 18598 99.37 %-
all-19781 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.245 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å2-0 Å20 Å2
2--0.56 Å2-0 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 18 90 2383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192368
X-RAY DIFFRACTIONr_bond_other_d0.0010.022347
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.9923179
X-RAY DIFFRACTIONr_angle_other_deg0.77635427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4895284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62325.221113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12115482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2331512
X-RAY DIFFRACTIONr_chiral_restr0.0750.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02516
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 73 -
Rwork0.266 1262 -
obs--96.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.50610.19890.26961.7531-0.97411.56140.04760.06940.04780.19180.05130.1553-0.3056-0.1143-0.09890.09130.04550.03150.08410.0440.04294.75532.4419-11.1973
21.31770.4801-1.00310.553-0.54721.63910.03810.1221-0.0265-0.1494-0.0014-0.03090.1105-0.0232-0.03670.07860.04020.00330.09460.00830.037816.7583-9.7401-21.8103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 141
2X-RAY DIFFRACTION2B3 - 139

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