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- PDB-2a4v: Crystal Structure of a truncated mutant of yeast nuclear thiol pe... -

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Basic information

Entry
Database: PDB / ID: 2a4v
TitleCrystal Structure of a truncated mutant of yeast nuclear thiol peroxidase
ComponentsPeroxiredoxin DOT5
KeywordsOXIDOREDUCTASE / yeast nuclear thiol peroxidase / atypical 2-Cys peroxiredoxin
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / cellular response to oxidative stress / chromosome, telomeric region / nucleus / 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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChoi, J. / Choi, S. / Chon, J.-K. / Choi, J. / Cha, M.-K. / Kim, I.-H. / Shin, W.
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of the C107S/C112S mutant of yeast nuclear 2-Cys peroxiredoxin
Authors: Choi, J. / Choi, S. / Chon, J.-K. / Choi, J. / Cha, M.-K. / Kim, I.-H. / Shin, W.
History
DepositionJun 29, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 10, 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 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxiredoxin DOT5


Theoretical massNumber of molelcules
Total (without water)17,8641
Polymers17,8641
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.535, 37.535, 83.256
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Peroxiredoxin DOT5 / Thioredoxin reductase / Nuclear thiol peroxidase / nTPx / Disrupter of telomere silencing protein 5


Mass: 17864.195 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN / Mutation: C107S/C112S/K123E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DOT5 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40553, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.91 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: PEG 3350, mercury(II) acetate, Tris-HCl, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal grow
*PLUS
pH: 7.4 / Details: Choi, J., (2005) Acta Crystallogr., F61, 659.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMTris-HCl1droppH7.4
320 %(w/v)PEG30001reservoir
4200 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714 Å
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Jan 1, 2005
RadiationMonochromator: double crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 12169 / Num. obs: 11928 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.085 / Χ2: 4.97 / Net I/σ(I): 12.4
Reflection shellResolution: 1.8→1.86 Å / % possible obs: 97 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.09 / Num. measured obs: 1173 / Num. unique all: 1171 / Rsym value: 0.321 / Χ2: 2.486 / % possible all: 97
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Num. measured all: 55862
Reflection shell
*PLUS
% possible obs: 97 % / Num. unique obs: 1171 / Num. measured obs: 5457 / Mean I/σ(I) obs: 3

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Phasing

Phasing MRRfactor: 0.57 / Cor.coef. Fo:Fc: 0.153
Highest resolutionLowest resolution
Rotation3 Å18.76 Å
Translation3 Å18.76 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.856 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.215 598 5 %RANDOM
Rwork0.165 ---
all0.167 12169 --
obs0.167 11928 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.279 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 0 156 1396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221263
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9831701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5445155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03124.82858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60915237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.593157
X-RAY DIFFRACTIONr_chiral_restr0.1050.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02945
X-RAY DIFFRACTIONr_nbd_refined0.2030.2627
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2877
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2118
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.215
X-RAY DIFFRACTIONr_mcbond_it0.9311.5805
X-RAY DIFFRACTIONr_mcangle_it1.42121265
X-RAY DIFFRACTIONr_scbond_it2.3123507
X-RAY DIFFRACTIONr_scangle_it3.6124.5436
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 43 -
Rwork0.218 798 -
all-841 -
obs-798 97 %
Software
*PLUS
Name: REFMAC / Version: 5.2.0005 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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