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- PDB-4xws: OxyR regulatory domain C199D mutant from pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4xws
TitleOxyR regulatory domain C199D mutant 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 3.006 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
DepositionJan 29, 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
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


Theoretical massNumber of molelcules
Total (without water)100,5724
Polymers100,5724
Non-polymers00
Water0
1
A: OxyR
B: OxyR


Theoretical massNumber of molelcules
Total (without water)50,2862
Polymers50,2862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-14 kcal/mol
Surface area19300 Å2
MethodPISA
2
C: OxyR
D: OxyR


Theoretical massNumber of molelcules
Total (without water)50,2862
Polymers50,2862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-15 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.942, 129.942, 135.692
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
OxyR


Mass: 25142.924 Da / Num. of mol.: 4 / Fragment: UNP residues 88-310 / Mutation: C199D
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

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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: 67.46 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris-HCl(9.0), 22% PEG 4k, 5mM DTT, 5mM TCEP / PH range: 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9783 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9783 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 25947 / % possible obs: 98.1 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 25.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 7.2 % / % possible all: 99.8

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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: 3.006→19.991 Å / SU ML: 0.44 / Cross valid method: NONE / σ(F): 1.51 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2604 1976 7.86 %
Rwork0.2293 --
obs0.2318 25142 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.006→19.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6176 0 0 0 6176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036353
X-RAY DIFFRACTIONf_angle_d0.8378683
X-RAY DIFFRACTIONf_dihedral_angle_d12.6472316
X-RAY DIFFRACTIONf_chiral_restr0.031005
X-RAY DIFFRACTIONf_plane_restr0.0051112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0057-3.08060.34471440.29961683X-RAY DIFFRACTION99
3.0806-3.16360.33831430.27991673X-RAY DIFFRACTION100
3.1636-3.25630.31161400.27541678X-RAY DIFFRACTION100
3.2563-3.36090.28031450.27031703X-RAY DIFFRACTION100
3.3609-3.48040.33481410.281679X-RAY DIFFRACTION99
3.4804-3.6190.28831410.28971637X-RAY DIFFRACTION96
3.619-3.78260.35461170.33691366X-RAY DIFFRACTION80
3.7826-3.98060.36791300.29781509X-RAY DIFFRACTION90
3.9806-4.22780.26551440.21041692X-RAY DIFFRACTION100
4.2278-4.55070.21261480.18381703X-RAY DIFFRACTION100
4.5507-5.00210.2251390.18051707X-RAY DIFFRACTION100
5.0021-5.71110.23521480.20511701X-RAY DIFFRACTION100
5.7111-7.14050.21851480.20671708X-RAY DIFFRACTION100
7.1405-19.99140.18331480.16971727X-RAY DIFFRACTION100

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