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- PDB-4i7h: Structural basis for peroxide sensing and gene regulation by PerR... -

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Basic information

Entry
Database: PDB / ID: 4i7h
TitleStructural basis for peroxide sensing and gene regulation by PerR from Streptococcus pyogenes
Componentsperoxide stress sensing regulator
KeywordsTRANSCRIPTION / winged helix-turn-helix motif / oxidative stress sensing / metal homeostasis / DNA
Function / homology
Function and homology information


DNA-binding transcription factor activity / metal ion binding
Similarity search - Function
Ferric-uptake regulator, C-terminal dimerisarion domain / Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / Dna Ligase; domain 1 / 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 / 2-Layer Sandwich ...Ferric-uptake regulator, C-terminal dimerisarion domain / Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / Dna Ligase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Putative ferric uptake regulator / Putative ferric uptake regulator
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKumaraswami, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal Structure of Peroxide Stress Regulator from Streptococcus pyogenes Provides Functional Insights into the Mechanism of Oxidative Stress Sensing.
Authors: Makthal, N. / Rastegari, S. / Sanson, M. / Ma, Z. / Olsen, R.J. / Helmann, J.D. / Musser, J.M. / Kumaraswami, M.
History
DepositionNov 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: peroxide stress sensing regulator
B: peroxide stress sensing regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0476
Polymers37,7992
Non-polymers2484
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-17 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.910, 118.910, 118.611
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-357-

HOH

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Components

#1: Protein peroxide stress sensing regulator / perR


Mass: 18899.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: ATCC BAA-595 / MGAS315 / Gene: spf, SpyM3_0147 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7CFI1, UniProt: A0A0H2UT39*PLUS
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2 M sodium chloride, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.110.9796, 0.957, 0.9798
SYNCHROTRONALS 8.3.121.116
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDAug 30, 2012
ADSC QUANTUM 3152CCDAug 30, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double flat crystal Si(111)MADMx-ray1
2double flat crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.9571
30.97981
41.1161
ReflectionResolution: 2→50 Å / Num. all: 33960 / Num. obs: 33859 / % possible obs: 99.7 %

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
SOLVEphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
ADSCQuantumdata collection
RefinementMethod to determine structure: MAD / Resolution: 2→47.231 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.57 / σ(F): 1.34 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 2000 5.91 %
Rwork0.2291 --
obs0.2312 33839 99.57 %
all-33984 -
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.334 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.8183 Å20 Å20 Å2
2---4.8183 Å2-0 Å2
3---9.6365 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2→47.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 4 152 2525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092417
X-RAY DIFFRACTIONf_angle_d1.1253277
X-RAY DIFFRACTIONf_dihedral_angle_d16.013895
X-RAY DIFFRACTIONf_chiral_restr0.091371
X-RAY DIFFRACTIONf_plane_restr0.005425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.34671400.2812236X-RAY DIFFRACTION99
2.05-2.10550.31871390.26372206X-RAY DIFFRACTION100
2.1055-2.16740.2671400.24782237X-RAY DIFFRACTION100
2.1674-2.23740.28111410.2472249X-RAY DIFFRACTION100
2.2374-2.31730.30771410.24992228X-RAY DIFFRACTION100
2.3173-2.41010.32951400.26592243X-RAY DIFFRACTION100
2.4101-2.51980.27491430.25452256X-RAY DIFFRACTION100
2.5198-2.65260.33371410.25082269X-RAY DIFFRACTION100
2.6526-2.81880.27591430.25122267X-RAY DIFFRACTION100
2.8188-3.03640.2981430.23992271X-RAY DIFFRACTION100
3.0364-3.34190.28311440.23692304X-RAY DIFFRACTION100
3.3419-3.82530.25431470.2122322X-RAY DIFFRACTION100
3.8253-4.81870.22221460.19262336X-RAY DIFFRACTION100
4.8187-47.24440.23411520.22722415X-RAY DIFFRACTION97
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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