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- PDB-3ixr: Crystal Structure of Xylella fastidiosa PrxQ C47S Mutant -

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Basic information

Entry
Database: PDB / ID: 3ixr
TitleCrystal Structure of Xylella fastidiosa PrxQ C47S Mutant
ComponentsBacterioferritin comigratory protein
KeywordsOXIDOREDUCTASE / Alpha Beta Protein
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / cellular response to oxidative stress / cytoplasm
Similarity search - Function
: / Peroxiredoxin, AhpC-type / 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
thioredoxin-dependent peroxiredoxin
Similarity search - Component
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHorta, B.B. / Oliveira, M.A. / Discola, K.F. / Cussiol, J.R.R. / Netto, L.E.S.
CitationJournal: To be Published
Title: Biochemical and Structural Analysis Indicates that PrxQ, a Cys Based Peroxidase from Xylella fastidiosa, possesses high reactivity towards hydroperoxides
Authors: Horta, B.B. / Oliveira, M.A. / Discola, K.F. / Cussiol, J.R.R. / Netto, L.E.S.
History
DepositionSep 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)19,9901
Polymers19,9901
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.973, 39.743, 99.836
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bacterioferritin comigratory protein / Peroxiredoxin PrxQ


Mass: 19989.652 Da / Num. of mol.: 1 / Mutation: C47S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (bacteria) / Strain: 9A5C / Gene: Peroxiredoxin Q, XF_0961 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q9PER7, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.93 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystallized in presence of 10 mM DTT. The optimal condition was obtained with the reservoir solution comprising 0.1 M Hepes-NaOH (pH 7.5) and 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.549 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 7, 2008 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.549 Å / Relative weight: 1
ReflectionResolution: 1.6→30.7 Å / Num. all: 20832 / Num. obs: 19697 / % possible obs: 98.01 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 6.1 / Redundancy: 13.3 % / Rsym value: 0.063 / Net I/σ(I): 6.3
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 6.1 / Rsym value: 0.36 / % possible all: 95.46

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1E2Y

1e2y


Resolution: 1.6→27.83 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 1.777 / SU ML: 0.063 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24669 1065 5.1 %RANDOM
Rwork0.19579 ---
obs0.19836 19695 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.433 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 0 171 1415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0221270
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3541.9451735
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0655167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54824.71753
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78715204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.404154
X-RAY DIFFRACTIONr_chiral_restr0.1820.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021958
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5121.5811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.44521309
X-RAY DIFFRACTIONr_scbond_it3.6163459
X-RAY DIFFRACTIONr_scangle_it5.3134.5421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 86 -
Rwork0.447 1382 -
obs--95.45 %

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