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- PDB-7cqj: Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/K84A/C207S/C2... -

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Basic information

Entry
Database: PDB / ID: 7cqj
TitlePeroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/K84A/C207S/C213S mutant (ApPrx*K84A)
ComponentsPeroxiredoxin
KeywordsOXIDOREDUCTASE / Peroxiredoxin
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
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
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionAug 11, 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
K: Peroxiredoxin
L: Peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)343,65312
Polymers343,65312
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60920 Å2
ΔGint-355 kcal/mol
Surface area91900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.008, 210.575, 308.668
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Peroxiredoxin / Thioredoxin peroxidase / ApTPx / Thioredoxin-dependent peroxiredoxin


Mass: 28637.727 Da / Num. of mol.: 12 / Mutation: C50S,K84A,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, thioredoxin-dependent peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The reservoir solution contained 0.10 M sodium acetate trihydrate (pH 4.6) 0.20 M calcium chloride dihydrate 20 %v/v 2-propanol.

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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: Feb 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→49.48 Å / Num. obs: 83831 / % possible obs: 99.9 % / Redundancy: 8.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.162 / Net I/σ(I): 8.9
Reflection shellResolution: 2.9→2.96 Å / Rmerge(I) obs: 0.965 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4559 / CC1/2: 0.763 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6krk

6krk


Resolution: 2.9→49.48 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.894 / SU B: 16.753 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R Free: 0.413
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2559 4355 5.199 %
Rwork0.1788 79408 -
all0.183 --
obs-83763 99.783 %
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: 52.418 Å2
Baniso -1Baniso -2Baniso -3
1-0.072 Å20 Å2-0 Å2
2---0.072 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23628 0 0 47 23675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01324288
X-RAY DIFFRACTIONr_bond_other_d0.0010.01722800
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.64633036
X-RAY DIFFRACTIONr_angle_other_deg1.2091.57452512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.76752916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.46919.8311416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.245153960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.90715264
X-RAY DIFFRACTIONr_chiral_restr0.070.23084
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0227144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025712
X-RAY DIFFRACTIONr_nbd_refined0.2090.25300
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.223286
X-RAY DIFFRACTIONr_nbtor_refined0.1720.211383
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.211984
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2536
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.140.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.220
X-RAY DIFFRACTIONr_nbd_other0.1640.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.26
X-RAY DIFFRACTIONr_mcbond_it4.225.28911700
X-RAY DIFFRACTIONr_mcbond_other4.225.28911699
X-RAY DIFFRACTIONr_mcangle_it6.3457.93214604
X-RAY DIFFRACTIONr_mcangle_other6.3457.93314605
X-RAY DIFFRACTIONr_scbond_it4.7225.82712588
X-RAY DIFFRACTIONr_scbond_other4.7225.82712589
X-RAY DIFFRACTIONr_scangle_it7.3058.52418432
X-RAY DIFFRACTIONr_scangle_other7.3058.52418433
X-RAY DIFFRACTIONr_lrange_it9.8161.2726806
X-RAY DIFFRACTIONr_lrange_other9.8161.27426807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.9750.3223110.2465839X-RAY DIFFRACTION100
2.975-3.0570.3252950.2325629X-RAY DIFFRACTION100
3.057-3.1450.3062790.2035556X-RAY DIFFRACTION100
3.145-3.2420.2842990.1995297X-RAY DIFFRACTION100
3.242-3.3480.3152800.1925244X-RAY DIFFRACTION99.9457
3.348-3.4660.2662610.1834992X-RAY DIFFRACTION100
3.466-3.5970.2472980.1654837X-RAY DIFFRACTION100
3.597-3.7440.2272620.1574664X-RAY DIFFRACTION99.9797
3.744-3.910.2562640.1614413X-RAY DIFFRACTION99.0051
3.91-4.1010.2632370.1634329X-RAY DIFFRACTION99.6508
4.101-4.3220.2152340.1544074X-RAY DIFFRACTION100
4.322-4.5840.2392430.1373838X-RAY DIFFRACTION100
4.584-4.9010.2042030.143697X-RAY DIFFRACTION100
4.901-5.2930.2571740.1653439X-RAY DIFFRACTION100
5.293-5.7980.2531610.1853194X-RAY DIFFRACTION100
5.798-6.4810.2381600.1582886X-RAY DIFFRACTION99.9344
6.481-7.4820.2291430.1492526X-RAY DIFFRACTION98.5598
7.482-9.1590.2221220.1692191X-RAY DIFFRACTION99.313
9.159-12.9350.248860.21737X-RAY DIFFRACTION99.1839
12.935-49.480.539430.5061026X-RAY DIFFRACTION96.1331

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