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- PDB-4y0m: The reduced form of OxyR regulatory domain from Psedomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4y0m
TitleThe reduced form of OxyR regulatory domain from Psedomonas 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 / 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 speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsJo, I. / Kim, J.S. / 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
DepositionFeb 6, 2015Deposition 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 / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list / struct_keywords
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 / _struct_keywords.text

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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
I: OxyR
J: OxyR
K: OxyR
L: OxyR


Theoretical massNumber of molelcules
Total (without water)303,82312
Polymers303,82312
Non-polymers00
Water5,693316
1
A: OxyR
B: OxyR


Theoretical massNumber of molelcules
Total (without water)50,6372
Polymers50,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-19 kcal/mol
Surface area18200 Å2
MethodPISA
2
C: OxyR
D: OxyR


Theoretical massNumber of molelcules
Total (without water)50,6372
Polymers50,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-17 kcal/mol
Surface area17700 Å2
MethodPISA
3
E: OxyR
F: OxyR


Theoretical massNumber of molelcules
Total (without water)50,6372
Polymers50,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-18 kcal/mol
Surface area17740 Å2
MethodPISA
4
G: OxyR
H: OxyR


Theoretical massNumber of molelcules
Total (without water)50,6372
Polymers50,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-19 kcal/mol
Surface area17620 Å2
MethodPISA
5
I: OxyR
J: OxyR


Theoretical massNumber of molelcules
Total (without water)50,6372
Polymers50,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-19 kcal/mol
Surface area17890 Å2
MethodPISA
6
K: OxyR
L: OxyR


Theoretical massNumber of molelcules
Total (without water)50,6372
Polymers50,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-18 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.355, 151.355, 218.844
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11I-408-

HOH

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Components

#1: Protein
OxyR


Mass: 25318.561 Da / Num. of mol.: 12 / Fragment: UNP residues 88-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: oxyR, PA5344 / Plasmid: pProEx-Hta / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HTL4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl(pH8.5), 24% PEG 4k, 2mM TCEP / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97952 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 127000 / % possible obs: 99.5 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 28.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.2 % / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
d*TREKdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→37.888 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 1.5 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 6321 5.02 %
Rwork0.2167 --
obs0.2194 125942 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→37.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19167 0 0 316 19483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819722
X-RAY DIFFRACTIONf_angle_d1.16626958
X-RAY DIFFRACTIONf_dihedral_angle_d12.0337216
X-RAY DIFFRACTIONf_chiral_restr0.0433119
X-RAY DIFFRACTIONf_plane_restr0.0053463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3004-2.32650.34192120.30453865X-RAY DIFFRACTION96
2.3265-2.35390.34072140.28863947X-RAY DIFFRACTION99
2.3539-2.38260.33811960.27983935X-RAY DIFFRACTION99
2.3826-2.41270.29352160.26553954X-RAY DIFFRACTION99
2.4127-2.44450.34412180.26743963X-RAY DIFFRACTION99
2.4445-2.4780.32922030.26873964X-RAY DIFFRACTION99
2.478-2.51340.32442000.26134007X-RAY DIFFRACTION100
2.5134-2.55090.32382020.25583942X-RAY DIFFRACTION99
2.5509-2.59070.29692040.24943983X-RAY DIFFRACTION99
2.5907-2.63320.30422020.24244000X-RAY DIFFRACTION99
2.6332-2.67860.31691870.24943975X-RAY DIFFRACTION99
2.6786-2.72730.32482220.24143996X-RAY DIFFRACTION100
2.7273-2.77970.26932220.22973962X-RAY DIFFRACTION100
2.7797-2.83640.30972230.23443989X-RAY DIFFRACTION100
2.8364-2.89810.30992140.23783985X-RAY DIFFRACTION100
2.8981-2.96550.30252040.24254039X-RAY DIFFRACTION100
2.9655-3.03960.28112290.25083948X-RAY DIFFRACTION100
3.0396-3.12180.34332100.24733992X-RAY DIFFRACTION100
3.1218-3.21360.28642200.24334013X-RAY DIFFRACTION100
3.2136-3.31720.2892090.23374022X-RAY DIFFRACTION100
3.3172-3.43570.26072080.22863995X-RAY DIFFRACTION100
3.4357-3.57320.27831900.21984013X-RAY DIFFRACTION100
3.5732-3.73570.26512100.21674045X-RAY DIFFRACTION100
3.7357-3.93240.2552290.19733992X-RAY DIFFRACTION100
3.9324-4.17850.23182150.18434025X-RAY DIFFRACTION100
4.1785-4.50070.22262160.1694039X-RAY DIFFRACTION100
4.5007-4.95270.21642210.15994024X-RAY DIFFRACTION100
4.9527-5.66730.21062190.17424039X-RAY DIFFRACTION100
5.6673-7.13240.25151890.1994099X-RAY DIFFRACTION100
7.1324-37.89340.22642170.17693869X-RAY DIFFRACTION93

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