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- PDB-4q77: Crystal structure of Rot, a global regulator of virulence genes i... -

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Basic information

Entry
Database: PDB / ID: 4q77
TitleCrystal structure of Rot, a global regulator of virulence genes in Staphylococcus aureus
ComponentsHTH-type transcriptional regulator rot
KeywordsDNA BINDING PROTEIN / Winged-helix motif / global regulator
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
HTH-type transcriptional regulator Rot / Transcriptional regulator SarA/Rot / : / Transcriptional regulator SarA/Rot / : / MarR family / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
HTH-type transcriptional regulator rot
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.77 Å
AuthorsZhu, Y. / Fan, X. / Li, X. / Teng, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of Rot, a global regulator of virulence genes in Staphylococcus aureus.
Authors: Zhu, Y. / Fan, X. / Zhang, X. / Jiang, X. / Niu, L. / Teng, M. / Li, X.
History
DepositionApr 24, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: HTH-type transcriptional regulator rot
B: HTH-type transcriptional regulator rot
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9863
Polymers32,8942
Non-polymers921
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-34 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.747, 71.505, 65.680
Angle α, β, γ (deg.)90.00, 99.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HTH-type transcriptional regulator rot / Repressor of toxins


Mass: 16446.875 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 34-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: rot, SAR1847 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GFT9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 285 K / Method: vapor diffusion / pH: 4.6
Details: 1.5M Ammonium chloride, 0.1M Sodium acetate trihydrate PH 4.6, VAPOR DIFFUSION, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.9791 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 17, 2014
RadiationMonochromator: NiFILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 27813

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→32.42 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.076 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 1396 5 %RANDOM
Rwork0.16315 ---
obs0.16588 26399 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.736 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0 Å2-0.37 Å2
2--1.68 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.77→32.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 6 140 2146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022033
X-RAY DIFFRACTIONr_bond_other_d0.0010.021985
X-RAY DIFFRACTIONr_angle_refined_deg1.0891.9662746
X-RAY DIFFRACTIONr_angle_other_deg0.74834553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5385246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.10525.28189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59715384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5091510
X-RAY DIFFRACTIONr_chiral_restr0.0640.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02442
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_it3.462.932996
X-RAY DIFFRACTIONr_mcbond_other3.462.931995
X-RAY DIFFRACTIONr_mcangle_it3.5764.3871238
X-RAY DIFFRACTIONr_mcangle_other3.5754.3871239
X-RAY DIFFRACTIONr_scbond_it4.0883.3871037
X-RAY DIFFRACTIONr_scbond_other4.0743.3861037
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9324.9321509
X-RAY DIFFRACTIONr_long_range_B_refined4.60224.2812455
X-RAY DIFFRACTIONr_long_range_B_other4.60424.2922456
X-RAY DIFFRACTIONr_rigid_bond_restr2.83134018
X-RAY DIFFRACTIONr_sphericity_free22.942550
X-RAY DIFFRACTIONr_sphericity_bonded11.96154081
LS refinement shellResolution: 1.767→1.813 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 100 -
Rwork0.178 1877 -
obs--97.1 %

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