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- PDB-6g4r: Corynebacterium glutamicum OxyR C206S mutant, H2O2-bound -

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Basic information

Entry
Database: PDB / ID: 6g4r
TitleCorynebacterium glutamicum OxyR C206S mutant, H2O2-bound
Components(Hydrogen peroxide-inducible genes ...) x 3
KeywordsTRANSCRIPTION / Hydrogen peroxide / redox / transcription factor / LysR
Function / homology
Function and homology information


protein-DNA complex / DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
HYDROGEN PEROXIDE / : / Probable hydrogen peroxide-inducible genes activator
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.62 Å
AuthorsYoung, D.R. / Pedre, B.P. / Messens, J.M.
Funding support Belgium, Spain, 5items
OrganizationGrant numberCountry
Other privateHERC16 Belgium
Other governmentG.0D79.14N Belgium
Other privateSRP34 Belgium
Other privateLE326U14 Spain
Other privateUXXI2016/00127 Spain
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural snapshots of OxyR reveal the peroxidatic mechanism of H2O2sensing.
Authors: Pedre, B. / Young, D. / Charlier, D. / Mourenza, A. / Rosado, L.A. / Marcos-Pascual, L. / Wahni, K. / Martens, E. / G de la Rubia, A. / Belousov, V.V. / Mateos, L.M. / Messens, J.
History
DepositionMar 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Hydrogen peroxide-inducible genes activator
A: Hydrogen peroxide-inducible genes activator
E: Hydrogen peroxide-inducible genes activator
G: Hydrogen peroxide-inducible genes activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,7209
Polymers140,4604
Non-polymers2605
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13660 Å2
ΔGint-89 kcal/mol
Surface area51170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.216, 56.991, 154.182
Angle α, β, γ (deg.)90.000, 98.020, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Hydrogen peroxide-inducible genes ... , 3 types, 4 molecules BAGE

#1: Protein Hydrogen peroxide-inducible genes activator


Mass: 35139.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: C0I99_13405 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H5I9R9, UniProt: Q8NP91*PLUS
#2: Protein Hydrogen peroxide-inducible genes activator


Mass: 35107.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: C0I99_13405 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H5I9R9, UniProt: Q8NP91*PLUS
#3: Protein Hydrogen peroxide-inducible genes activator


Mass: 35107.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: C0I99_13405 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H5I9R9, UniProt: Q8NP91*PLUS

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Non-polymers , 4 types, 110 molecules

#4: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 4000, 2-(N-morpholino)ethanesulfonic acid (MES), lithium sulfate, TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→153 Å / Num. obs: 37454 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 47.81 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.105 / Rrim(I) all: 0.268 / Net I/σ(I): 5.3 / Num. measured all: 241902 / Scaling rejects: 125
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.62-2.696.52.0391793127620.3360.8612.2171.4100
11.72-15360.10327594630.9830.0460.11312.799.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.62→76.34 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs36733 99.8 %
Refinement stepCycle: LAST / Resolution: 2.62→76.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9122 0 15 105 9242
LS refinement shellResolution: 2.62→2.71 Å
RfactorNum. reflection% reflection
Rfree0.465 178 5.4 %
Rwork0.413 3460 -
obs--93.09 %

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