[English] 日本語
Yorodumi
- PDB-2vl9: Oxidized form of human peroxiredoxin 5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vl9
TitleOxidized form of human peroxiredoxin 5
ComponentsPEROXIREDOXIN-5
KeywordsOXIDOREDUCTASE / THIOREDOXIN PEROXIDASE / ALTERNATIVE INITIATION / ANTIOXIDANT ENZYME / REDOX-ACTIVE CENTER / CYTOPLASM / PEROXIDASE / PEROXISOME / ANTIOXIDANT / POLYMORPHISM / MITOCHONDRION / PEROXIREDOXIN / TRANSIT PEPTIDE / THIOREDOXIN FOLD
Function / homology
Function and homology information


peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of oxidoreductase activity / negative regulation of transcription by RNA polymerase III / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Detoxification of Reactive Oxygen Species ...peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of oxidoreductase activity / negative regulation of transcription by RNA polymerase III / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Detoxification of Reactive Oxygen Species / antioxidant activity / peroxisomal matrix / positive regulation of collagen biosynthetic process / cell redox homeostasis / cellular response to reactive oxygen species / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / peroxidase activity / peroxisome / response to oxidative stress / cellular response to oxidative stress / cytoplasmic vesicle / mitochondrial matrix / inflammatory response / signaling receptor binding / intracellular membrane-bounded organelle / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / extracellular space / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Peroxiredoxin-5-like / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peroxiredoxin-5, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSmeets, A. / Declercq, J.P.
CitationJournal: Arch.Biochem.Biophys. / Year: 2008
Title: The Crystal Structures of Oxidized Forms of Human Peroxiredoxin 5 with an Intramolecular Disulfide Bond Confirm the Proposed Enzymatic Mechanism for Atypical 2-Cys Peroxiredoxins.
Authors: Smeets, A. / Marchand, C. / Linard, D. / Knoops, B. / Declercq, J.P.
History
DepositionJan 11, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PEROXIREDOXIN-5
B: PEROXIREDOXIN-5
C: PEROXIREDOXIN-5
D: PEROXIREDOXIN-5


Theoretical massNumber of molelcules
Total (without water)73,2364
Polymers73,2364
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-38.6 kcal/mol
Surface area34250 Å2
MethodPQS
Unit cell
Length a, b, c (Å)75.870, 75.870, 193.254
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein
PEROXIREDOXIN-5 / PRX-V / PEROXISOMAL ANTIOXIDANT ENZYME / PLP / THIOREDOXIN REDUCTASE / THIOREDOXIN PEROXIDASE PMP20 ...PRX-V / PEROXISOMAL ANTIOXIDANT ENZYME / PLP / THIOREDOXIN REDUCTASE / THIOREDOXIN PEROXIDASE PMP20 / ANTIOXIDANT ENZYME B166 / AOEB166 / TPX TYPE VI / LIVER TISSUE 2D-PAGE SPOT 71B / ALU COREPRESSOR 1 / HUMAN PEROXIREDOXIN 5


Mass: 18308.979 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-162 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LUNG / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: P30044, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 73 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 73 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 73 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 73 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 73 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 73 TO SER
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.53 %
Description: THE MODEL USED FOR THE MOLECULAR REPLACEMENT WAS A SIMULATION CREATED FROM PDB ENTRY 1OC3
Crystal growpH: 6.5
Details: PEG 8000 20% SODIUM CACODYLATE 0.1 M PH 6.5 SODIUM ACETATE 0.1 M 6-AMINOCAPROIC ACID 3% W/V

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979764
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 11, 2005 / Details: TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING
RadiationMonochromator: FIRST CRYSTAL FLAT AND N2 COOLED. SECOND ONE SAGITALLY BENT
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979764 Å / Relative weight: 1
Reflection twinOperator: -K,H+K,L / Fraction: 0.479
ReflectionResolution: 2.7→46 Å / Num. obs: 18076 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 4.05 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.9
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 4.05 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.4 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OC3

1oc3


Resolution: 2.7→46 Å / Phase error: 24.5 / Stereochemistry target values: TWIN_LSQ_F
Details: TWIN RATIO IS 50%. COMPUTED STRUCTURE FACTORS ARE NOT DIRECTLY COMPARABLE TO THE DEPOSITED OBSERVED STRUCTURE FACTORS.
RfactorNum. reflection% reflection
Rfree0.239 923 5.1 %
Rwork0.1836 --
obs0.1863 18076 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 170.46 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 79.53 Å2
Baniso -1Baniso -2Baniso -3
1--6.4257 Å2-0 Å20 Å2
2---6.4257 Å2-0 Å2
3---12.6603 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 0 57 4817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064836
X-RAY DIFFRACTIONf_angle_d1.6366539
X-RAY DIFFRACTIONf_dihedral_angle_d19.5691766
X-RAY DIFFRACTIONf_chiral_restr0.104760
X-RAY DIFFRACTIONf_plane_restr0.007853

+
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