[English] 日本語
Yorodumi
- PDB-7c87: Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c87
TitlePeroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C213S mutant (ApPrx*F80C)
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
CITRIC ACID / Peroxiredoxin
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)288,43920
Polymers286,51810
Non-polymers1,92110
Water16,141896
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53200 Å2
ΔGint-275 kcal/mol
Surface area77440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.065, 103.134, 104.956
Angle α, β, γ (deg.)106.026, 104.752, 92.595
Int Tables number1
Space group name H-MP1

-
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 896 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.59 %
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.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 146036 / % possible obs: 97.7 % / Redundancy: 2.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 7276 / CC1/2: 0.927

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KRK

6krk


Resolution: 2.2→49.227 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.108 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.181
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2072 7443 5.107 %
Rwork0.1564 138301 -
all0.159 --
obs-145744 97.546 %
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: 44.523 Å2
Baniso -1Baniso -2Baniso -3
1-0.006 Å2-0.002 Å20.004 Å2
2---0.005 Å2-0.002 Å2
3----0.002 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19680 0 130 896 20706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01320340
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719070
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.64727660
X-RAY DIFFRACTIONr_angle_other_deg1.3041.57543960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87652430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.5819.8291170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.519153340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.55415220
X-RAY DIFFRACTIONr_chiral_restr0.0760.22570
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024710
X-RAY DIFFRACTIONr_nbd_refined0.2030.24182
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.219129
X-RAY DIFFRACTIONr_nbtor_refined0.1680.29791
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.29812
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2856
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.226
X-RAY DIFFRACTIONr_nbd_other0.2430.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.240.222
X-RAY DIFFRACTIONr_mcbond_it3.3984.3859750
X-RAY DIFFRACTIONr_mcbond_other3.3974.3849749
X-RAY DIFFRACTIONr_mcangle_it4.4996.5612170
X-RAY DIFFRACTIONr_mcangle_other4.4996.56112171
X-RAY DIFFRACTIONr_scbond_it4.7074.9410590
X-RAY DIFFRACTIONr_scbond_other4.7074.9410587
X-RAY DIFFRACTIONr_scangle_it6.9037.18115490
X-RAY DIFFRACTIONr_scangle_other6.9037.18115491
X-RAY DIFFRACTIONr_lrange_it8.59551.25722822
X-RAY DIFFRACTIONr_lrange_other8.59151.10722698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.2635600.20810162X-RAY DIFFRACTION96.5772
2.257-2.3190.2355190.1859891X-RAY DIFFRACTION96.6305
2.319-2.3860.2295300.1769610X-RAY DIFFRACTION96.6451
2.386-2.460.2214980.1699367X-RAY DIFFRACTION96.9247
2.46-2.540.2384510.1759057X-RAY DIFFRACTION96.9512
2.54-2.6290.2455040.1838791X-RAY DIFFRACTION97.096
2.629-2.7280.2544490.1748526X-RAY DIFFRACTION97.4802
2.728-2.840.264380.1818190X-RAY DIFFRACTION97.5025
2.84-2.9660.2324290.177820X-RAY DIFFRACTION97.6907
2.966-3.110.2314000.1697537X-RAY DIFFRACTION97.6862
3.11-3.2790.2254060.1597161X-RAY DIFFRACTION97.6639
3.279-3.4770.2193400.1626803X-RAY DIFFRACTION97.7957
3.477-3.7170.2163350.1526373X-RAY DIFFRACTION98.3866
3.717-4.0140.1723430.1385997X-RAY DIFFRACTION98.8309
4.014-4.3970.1672850.1285502X-RAY DIFFRACTION98.9062
4.397-4.9140.1642710.124998X-RAY DIFFRACTION98.837
4.914-5.6720.1772330.1374399X-RAY DIFFRACTION99.0167
5.672-6.9410.1992000.1493728X-RAY DIFFRACTION98.7431
6.941-9.7920.1441640.1262832X-RAY DIFFRACTION98.6825
9.792-49.2270.193880.1921557X-RAY DIFFRACTION96.651

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more