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- PDB-5b70: OxyR2 E204G regulatory domain from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 5b70
TitleOxyR2 E204G regulatory domain from Vibrio vulnificus
ComponentsLysR family transcriptional regulator
KeywordsTRANSCRIPTION / LysR-type transcription regulator / LTTR / OxyR / H2O2
Function / homology
Function and homology information


protein-DNA complex / DNA-binding transcription factor activity / DNA binding
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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hydrogen peroxide-inducible genes activator
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsJo, I. / Ha, N.-C.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The hydrogen peroxide hypersensitivity of OxyR2 in Vibrio vulnificus depends on conformational constraints
Authors: Jo, I. / Kim, D. / Bang, Y.-J. / Ahn, J. / Choi, S.H. / Ha, N.-C.
History
DepositionJun 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LysR family transcriptional regulator
B: LysR family transcriptional regulator
C: LysR family transcriptional regulator
D: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4876
Polymers96,3034
Non-polymers1842
Water3,117173
1
A: LysR family transcriptional regulator
D: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2443
Polymers48,1522
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-27 kcal/mol
Surface area17590 Å2
MethodPISA
2
B: LysR family transcriptional regulator
C: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2443
Polymers48,1522
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-23 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.375, 141.375, 109.664
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11D-269-

GLY

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Components

#1: Protein
LysR family transcriptional regulator


Mass: 24075.781 Da / Num. of mol.: 4 / Fragment: UNP residues 86-301 / Mutation: E204G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: MO6-24/O / Production host: Escherichia coli (E. coli) / References: UniProt: A0A087I947
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.29 Å3/Da / Density % sol: 62.56 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.2M sodium acetate, 0.1M Tris-HCl (pH 9.0), 14% PEG 4000, 2mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.3→33.96 Å / Num. obs: 53831 / % possible obs: 95.31 % / Redundancy: 5.6 % / Biso Wilson estimate: 28.69 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.67
Reflection shellResolution: 2.3→2.62 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.46 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.3→33.957 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 28.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2675 2007 3.73 %
Rwork0.2278 --
obs0.2293 53827 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→33.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6551 0 12 173 6736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036686
X-RAY DIFFRACTIONf_angle_d0.5869075
X-RAY DIFFRACTIONf_dihedral_angle_d12.34107
X-RAY DIFFRACTIONf_chiral_restr0.0441086
X-RAY DIFFRACTIONf_plane_restr0.0041177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.37361120.35992972X-RAY DIFFRACTION77
2.3575-2.42120.36241230.35033271X-RAY DIFFRACTION85
2.4212-2.49250.38531340.33393512X-RAY DIFFRACTION91
2.4925-2.57290.3661350.33343613X-RAY DIFFRACTION95
2.5729-2.66480.36351440.32183740X-RAY DIFFRACTION96
2.6648-2.77150.35361460.30683741X-RAY DIFFRACTION97
2.7715-2.89750.36441520.2963768X-RAY DIFFRACTION98
2.8975-3.05020.31261500.27083781X-RAY DIFFRACTION98
3.0502-3.24120.30071470.24423836X-RAY DIFFRACTION99
3.2412-3.49120.25241480.22543853X-RAY DIFFRACTION100
3.4912-3.84210.25041540.20213888X-RAY DIFFRACTION100
3.8421-4.3970.21021500.16463897X-RAY DIFFRACTION100
4.397-5.53590.19841570.15063892X-RAY DIFFRACTION100
5.5359-33.96090.1911550.16564056X-RAY DIFFRACTION99

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