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- PDB-5iox: Xanthomonas campestris Peroxiredoxin Q - Structure LUss -

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Basic information

Entry
Database: PDB / ID: 5iox
TitleXanthomonas campestris Peroxiredoxin Q - Structure LUss
ComponentsBacterioferritin comigratory protein
KeywordsOXIDOREDUCTASE / PrxQ / BCP / Peroxidase / redox
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / cellular response to oxidative stress / cytoplasm
Similarity search - Function
: / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPerkins, A. / Parsonage, D. / Nelson, K.J. / Poole, L.B. / Karplus, A.
CitationJournal: Structure / Year: 2016
Title: Peroxiredoxin Catalysis at Atomic Resolution.
Authors: Perkins, A. / Parsonage, D. / Nelson, K.J. / Ogba, O.M. / Cheong, P.H. / Poole, L.B. / Karplus, P.A.
History
DepositionMar 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterioferritin comigratory protein


Theoretical massNumber of molelcules
Total (without water)17,3001
Polymers17,3001
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.650, 54.130, 36.610
Angle α, β, γ (deg.)90.00, 107.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bacterioferritin comigratory protein


Mass: 17299.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25) (bacteria)
Strain: ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25 / Gene: XCC1738 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8P9V9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.89 Å3/Da / Density % sol: 34.94 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 1.0 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M sodium cacodylate pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.96486 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96486 Å / Relative weight: 1
ReflectionResolution: 1.3→34.87 Å / Num. obs: 28974 / % possible obs: 91.4 % / Redundancy: 6 % / CC1/2: 0.314 / Net I/σ(I): 8
Reflection shellHighest resolution: 1.3 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3gkk

3gkk


Resolution: 1.3→33.006 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.21
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 1481 5.1 %Imported from 3gkk
Rwork0.1818 ---
obs0.1834 28974 89.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→33.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 0 125 1298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091220
X-RAY DIFFRACTIONf_angle_d1.2961654
X-RAY DIFFRACTIONf_dihedral_angle_d13.508435
X-RAY DIFFRACTIONf_chiral_restr0.081187
X-RAY DIFFRACTIONf_plane_restr0.006214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.32240.3687760.38261426X-RAY DIFFRACTION48
1.3224-1.34650.3573760.36641698X-RAY DIFFRACTION57
1.3465-1.37240.4063830.35682003X-RAY DIFFRACTION66
1.3724-1.40040.38861220.33892298X-RAY DIFFRACTION77
1.4004-1.43080.33541310.32862515X-RAY DIFFRACTION86
1.4308-1.46410.32631180.30162767X-RAY DIFFRACTION92
1.4641-1.50070.32761790.26242836X-RAY DIFFRACTION97
1.5007-1.54130.28821740.23492830X-RAY DIFFRACTION97
1.5413-1.58670.25241670.21262873X-RAY DIFFRACTION97
1.5867-1.63790.25241500.20322906X-RAY DIFFRACTION97
1.6379-1.69640.22491450.21132870X-RAY DIFFRACTION97
1.6964-1.76430.2431440.20332880X-RAY DIFFRACTION98
1.7643-1.84460.22611570.18872899X-RAY DIFFRACTION98
1.8446-1.94190.22821600.18482894X-RAY DIFFRACTION98
1.9419-2.06350.20461520.16812904X-RAY DIFFRACTION98
2.0635-2.22280.18641350.16742919X-RAY DIFFRACTION98
2.2228-2.44640.1931540.15882913X-RAY DIFFRACTION97
2.4464-2.80030.18421820.16972812X-RAY DIFFRACTION97
2.8003-3.52740.2181700.15572852X-RAY DIFFRACTION97
3.5274-33.01670.16781720.14572915X-RAY DIFFRACTION99

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