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- PDB-7c89: Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C2... -

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Basic information

Entry
Database: PDB / ID: 7c89
TitlePeroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C213S mutant modified with 2-bromoacetophenone(Ph@ApPrx*)
ComponentsPeroxiredoxin
KeywordsOXIDOREDUCTASE / Peroxiredoxin
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin activity / thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / antioxidant activity / cellular response to hydrogen peroxide / identical protein binding / cytoplasm
Similarity search - Function
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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
2-bromanyl-1-phenyl-ethanone / CITRATE ANION / Peroxiredoxin
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHimiyama, T. / Nakamura, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K21133 Japan
Japan Society for the Promotion of Science (JSPS)20K15403 Japan
CitationJournal: Bioconjug.Chem. / Year: 2021
Title: Rebuilding Ring-Type Assembly of Peroxiredoxin by Chemical Modification.
Authors: Himiyama, T. / Tsuchiya, Y. / Yonezawa, Y. / Nakamura, T.
History
DepositionMay 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin
B: Peroxiredoxin
C: Peroxiredoxin
D: Peroxiredoxin
E: Peroxiredoxin
F: Peroxiredoxin
G: Peroxiredoxin
H: Peroxiredoxin
I: Peroxiredoxin
J: Peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,39930
Polymers286,51810
Non-polymers3,88120
Water20,6451146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54550 Å2
ΔGint-296 kcal/mol
Surface area77050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.035, 102.986, 105.169
Angle α, β, γ (deg.)106.002, 104.756, 92.548
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Peroxiredoxin / / Thioredoxin peroxidase / ApTPx


Mass: 28651.797 Da / Num. of mol.: 10 / Mutation: C50S, F80C, C207S, C213S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Strain: K1 / Gene: APE_2278 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y9L0, peroxiredoxin
#2: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-FL0 / 2-bromanyl-1-phenyl-ethanone / Phenacyl bromide


Mass: 199.045 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H7BrO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The reservoir solution contained 0.10 M sodium citrate (pH5.5) 0.20 M lithium sulfate 15% (v/v) reagent alcohol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 168919 / % possible obs: 98.3 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.1
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3 / Num. unique obs: 8244 / CC1/2: 0.889

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KRK

6krk


Resolution: 2.1→49.168 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.406 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.163
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2101 8400 4.973 %
Rwork0.1591 160516 -
all0.162 --
obs-168916 98.328 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 33.297 Å2
Baniso -1Baniso -2Baniso -3
1--0.011 Å20.002 Å20.001 Å2
2--0.008 Å20.006 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19680 0 220 1146 21046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01320440
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719140
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.65427790
X-RAY DIFFRACTIONr_angle_other_deg1.3421.57944110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85452430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.50919.8291170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.945153340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.45715220
X-RAY DIFFRACTIONr_chiral_restr0.080.22570
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222780
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024760
X-RAY DIFFRACTIONr_nbd_refined0.2030.24575
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.219988
X-RAY DIFFRACTIONr_nbtor_refined0.1720.29920
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.29923
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.21061
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1820.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.240
X-RAY DIFFRACTIONr_nbd_other0.2620.2126
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1990.213
X-RAY DIFFRACTIONr_mcbond_it2.5963.1989750
X-RAY DIFFRACTIONr_mcbond_other2.5943.1979749
X-RAY DIFFRACTIONr_mcangle_it3.6654.77612170
X-RAY DIFFRACTIONr_mcangle_other3.6644.77712171
X-RAY DIFFRACTIONr_scbond_it3.9293.710690
X-RAY DIFFRACTIONr_scbond_other3.9293.710691
X-RAY DIFFRACTIONr_scangle_it6.0275.34515620
X-RAY DIFFRACTIONr_scangle_other6.0265.34515621
X-RAY DIFFRACTIONr_lrange_it7.91238.33323570
X-RAY DIFFRACTIONr_lrange_other7.89738.11123377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.2686120.21911758X-RAY DIFFRACTION97.302
2.155-2.2140.2555810.20711440X-RAY DIFFRACTION97.4702
2.214-2.2780.2495900.19211242X-RAY DIFFRACTION97.5916
2.278-2.3480.2325560.17810864X-RAY DIFFRACTION97.7071
2.348-2.4250.2525360.17710496X-RAY DIFFRACTION97.8535
2.425-2.510.2425010.16310325X-RAY DIFFRACTION98.0527
2.51-2.6040.2195280.1659802X-RAY DIFFRACTION98.0914
2.604-2.7110.2144940.1649543X-RAY DIFFRACTION98.2382
2.711-2.8310.2344560.1719140X-RAY DIFFRACTION98.3701
2.831-2.9690.2314760.1668724X-RAY DIFFRACTION98.6066
2.969-3.130.2284470.1668317X-RAY DIFFRACTION98.6493
3.13-3.3190.2044080.1577910X-RAY DIFFRACTION98.859
3.319-3.5480.2073820.1557381X-RAY DIFFRACTION98.9295
3.548-3.8320.1953670.1486932X-RAY DIFFRACTION99.1308
3.832-4.1970.1783560.1386363X-RAY DIFFRACTION99.2027
4.197-4.6910.1663170.1215734X-RAY DIFFRACTION99.3759
4.691-5.4150.1682810.1255106X-RAY DIFFRACTION99.4462
5.415-6.6270.2162210.1524291X-RAY DIFFRACTION99.6027
6.627-9.3510.1521940.1393321X-RAY DIFFRACTION99.7163
9.351-49.1680.256970.1991827X-RAY DIFFRACTION99.1753

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