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- PDB-2nvl: Crystal structure of archaeal peroxiredoxin, thioredoxin peroxida... -

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Basic information

Entry
Database: PDB / ID: 2nvl
TitleCrystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfonic acid form)
ComponentsProbable peroxiredoxin
KeywordsOXIDOREDUCTASE / cysteine sulfenic acid / cysteine sulfinic acid / cysteine sulfonic acid / hypervalent sulfur compound / peroxidatic cysteine
Function / homology
Function and homology information


peroxiredoxin activity / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / antioxidant activity / cell redox homeostasis / hydrogen peroxide catabolic process / cellular response to hydrogen peroxide / identical protein binding / cytosol
Similarity search - Function
Antioxidant, Horf6; Chain A, domain 2 / Antioxidant, Horf6; Chain A, domain2 / Peroxiredoxin, TDXH subfamily / 1-Cys peroxiredoxin / Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family ...Antioxidant, Horf6; Chain A, domain 2 / Antioxidant, Horf6; Chain A, domain2 / Peroxiredoxin, TDXH subfamily / 1-Cys peroxiredoxin / Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsNakamura, T. / Yamamoto, T. / Abe, M. / Matsumura, H. / Hagihara, Y. / Goto, T. / Yamaguchi, T. / Inoue, T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate
Authors: Nakamura, T. / Yamamoto, T. / Abe, M. / Matsumura, H. / Hagihara, Y. / Goto, T. / Yamaguchi, T. / Inoue, T.
History
DepositionNov 13, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable peroxiredoxin
B: Probable peroxiredoxin
C: Probable peroxiredoxin
D: Probable peroxiredoxin
E: Probable peroxiredoxin
F: Probable peroxiredoxin
G: Probable peroxiredoxin
H: Probable peroxiredoxin
I: Probable peroxiredoxin
J: Probable peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)287,76010
Polymers287,76010
Non-polymers00
Water12,701705
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48010 Å2
ΔGint-313.3 kcal/mol
Surface area77060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.319, 102.962, 104.300
Angle α, β, γ (deg.)105.65, 105.26, 92.69
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Probable peroxiredoxin / Thioredoxin peroxidase


Mass: 28775.953 Da / Num. of mol.: 10 / Mutation: C207S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9Y9L0, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M sodium acetate pH4.8, 0.2M calcium chloride, 10%(v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 120463 / % possible obs: 97 % / Redundancy: 2.1 % / Net I/σ(I): 8.7
Reflection shellResolution: 2.35→2.43 Å / % possible all: 87.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X0R

1x0r


Resolution: 2.36→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.354 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21901 5902 5.1 %RANDOM
Rwork0.16619 ---
obs0.1688 110905 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.553 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0.5 Å21.09 Å2
2---1.6 Å2-0.31 Å2
3---1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.36→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19623 0 0 705 20328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02220172
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.95927449
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29152404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9222.086959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.016153328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.52515220
X-RAY DIFFRACTIONr_chiral_restr0.1310.22975
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215528
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2480.210057
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.213580
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.21026
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2860.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4741.512469
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.226219657
X-RAY DIFFRACTIONr_scbond_it3.47938933
X-RAY DIFFRACTIONr_scangle_it5.4114.57792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.36→2.417 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 382 -
Rwork0.216 6831 -
obs--80.71 %

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