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- PDB-4x6g: Full-length OxyR C199D from pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4x6g
TitleFull-length OxyR C199D from pseudomonas aeruginosa
ComponentsOxyR
KeywordsDNA BINDING PROTEIN / OxyR / peroxide / Transcription regulator / LysR
Function / homology
Function and homology information


regulation of response to reactive oxygen species / negative regulation of secondary metabolite biosynthetic process / positive regulation of cell motility / positive regulation of lipid biosynthetic process / protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HYDROGEN PEROXIDE / Hydrogen peroxide-inducible genes activator
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJo, I. / Ha, N.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural details of the OxyR peroxide-sensing mechanism
Authors: Jo, I. / Chung, I.Y. / Bae, H.W. / Kim, J.S. / Song, S. / Cho, Y.H. / Ha, N.C.
History
DepositionDec 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2May 16, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_beamline ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 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: OxyR
B: OxyR
C: OxyR
D: OxyR
E: OxyR
F: OxyR
G: OxyR
H: OxyR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,08031
Polymers281,4278
Non-polymers1,65423
Water20,5731142
1
A: OxyR
B: OxyR
C: OxyR
D: OxyR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,77018
Polymers140,7134
Non-polymers1,05714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13580 Å2
ΔGint-72 kcal/mol
Surface area52150 Å2
MethodPISA
2
E: OxyR
F: OxyR
G: OxyR
H: OxyR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,31013
Polymers140,7134
Non-polymers5979
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12150 Å2
ΔGint-81 kcal/mol
Surface area51930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.636, 151.129, 141.581
Angle α, β, γ (deg.)90.00, 97.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
OxyR / peroxide sensing transcription regulator


Mass: 35178.363 Da / Num. of mol.: 8 / Mutation: C199D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: oxyR, PA5344 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HTL4
#2: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1142 / 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: 3.28 Å3/Da / Density % sol: 62.45 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2M Sodium citrate tribasic (pH 8.3), 14% PEG 3350, 2mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 172391 / % possible obs: 95.3 % / Redundancy: 4.2 % / Net I/σ(I): 13.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.5 % / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
d*TREKdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.965 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2366 8649 5.02 %
Rwork0.1856 --
obs0.1882 172391 75.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18513 0 106 1142 19761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01319079
X-RAY DIFFRACTIONf_angle_d1.49625940
X-RAY DIFFRACTIONf_dihedral_angle_d14.4927092
X-RAY DIFFRACTIONf_chiral_restr0.0572992
X-RAY DIFFRACTIONf_plane_restr0.0083358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.1494140.2419156X-RAY DIFFRACTION2
2.0227-2.04640.3032180.2397346X-RAY DIFFRACTION5
2.0464-2.07140.2978410.2549711X-RAY DIFFRACTION10
2.0714-2.09760.262590.2571194X-RAY DIFFRACTION16
2.0976-2.12510.25581010.24071863X-RAY DIFFRACTION26
2.1251-2.15420.31351220.24342595X-RAY DIFFRACTION36
2.1542-2.1850.31671820.25283376X-RAY DIFFRACTION47
2.185-2.21750.27371910.23383952X-RAY DIFFRACTION54
2.2175-2.25210.32822440.26065096X-RAY DIFFRACTION70
2.2521-2.2890.312970.24575335X-RAY DIFFRACTION74
2.289-2.32840.29522980.2365887X-RAY DIFFRACTION81
2.3284-2.37070.33183040.23556297X-RAY DIFFRACTION87
2.3707-2.41620.28463650.22826467X-RAY DIFFRACTION90
2.4162-2.46540.31893620.22466727X-RAY DIFFRACTION93
2.4654-2.51890.28293860.22866885X-RAY DIFFRACTION95
2.5189-2.57740.28453330.22626915X-RAY DIFFRACTION95
2.5774-2.64170.27313490.21726974X-RAY DIFFRACTION96
2.6417-2.7130.26963640.21957023X-RAY DIFFRACTION97
2.713-2.79260.27663870.21996994X-RAY DIFFRACTION97
2.7926-2.88250.23973460.21457082X-RAY DIFFRACTION97
2.8825-2.98520.2563730.22087010X-RAY DIFFRACTION97
2.9852-3.10430.28373960.21047131X-RAY DIFFRACTION98
3.1043-3.2450.24223520.20027191X-RAY DIFFRACTION99
3.245-3.41530.24663840.19497162X-RAY DIFFRACTION99
3.4153-3.62810.22223890.17087173X-RAY DIFFRACTION99
3.6281-3.90630.20114200.15547230X-RAY DIFFRACTION99
3.9063-4.29590.19313770.13917209X-RAY DIFFRACTION99
4.2959-4.90940.17554080.12337177X-RAY DIFFRACTION99
4.9094-6.15510.18494120.14287265X-RAY DIFFRACTION100
6.1551-19.96570.19413750.14637319X-RAY DIFFRACTION99

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