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- PDB-5j9b: Crystal structure of peroxiredoxin Asp f3 -

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Basic information

Entry
Database: PDB / ID: 5j9b
TitleCrystal structure of peroxiredoxin Asp f3
Componentsperoxiredoxin Asp f3
KeywordsOXIDOREDUCTASE / peroxiredoxin / Aspergillus
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / IgE binding / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / cellular response to oxidative stress / protein homodimerization activity / mitochondrion / cytoplasm
Similarity search - Function
Peroxiredoxin-5-like / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peroxiredoxin Asp f3
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBzymek, K.P. / Williams, J.C. / Hong, T.B. / Bagramyan, K. / Kalkum, M.
CitationJournal: Sci Rep / Year: 2016
Title: The Crystal Structure of Peroxiredoxin Asp f3 Provides Mechanistic Insight into Oxidative Stress Resistance and Virulence of Aspergillus fumigatus.
Authors: Hillmann, F. / Bagramyan, K. / Straburger, M. / Heinekamp, T. / Hong, T.B. / Bzymek, K.P. / Williams, J.C. / Brakhage, A.A. / Kalkum, M.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: peroxiredoxin Asp f3
B: peroxiredoxin Asp f3


Theoretical massNumber of molelcules
Total (without water)38,7222
Polymers38,7222
Non-polymers00
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-12 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.980, 68.490, 89.450
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 peroxiredoxin Asp f3 / Peroxisomal membrane protein pmp20 / Thioredoxin reductase


Mass: 19360.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: pmp20, AFUA_6G02280 / Production host: Escherichia coli (E. coli) / References: UniProt: O43099, peroxiredoxin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 MES pH 6.5, 27% PEG 3350, 25 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→32 Å / Num. obs: 19588 / % possible obs: 99.8 % / Redundancy: 4.6 % / CC1/2: 0.991 / Net I/σ(I): 9.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.99 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F82

4f82


Resolution: 2.1→31.981 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.31
RfactorNum. reflection% reflection
Rfree0.2469 979 5 %
Rwork0.1828 --
obs0.1859 19584 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→31.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 0 264 2814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072632
X-RAY DIFFRACTIONf_angle_d1.0813580
X-RAY DIFFRACTIONf_dihedral_angle_d13.059934
X-RAY DIFFRACTIONf_chiral_restr0.045393
X-RAY DIFFRACTIONf_plane_restr0.005458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.21080.2911390.22372642X-RAY DIFFRACTION100
2.2108-2.34920.27461370.21812596X-RAY DIFFRACTION100
2.3492-2.53060.2941380.21552631X-RAY DIFFRACTION100
2.5306-2.78510.27651380.20292620X-RAY DIFFRACTION100
2.7851-3.18780.24791390.19122639X-RAY DIFFRACTION100
3.1878-4.0150.21461420.16172685X-RAY DIFFRACTION100
4.015-31.98510.21881460.15282792X-RAY DIFFRACTION99

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