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- PDB-2vl2: Oxidized and reduced forms of human peroxiredoxin 5 -

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Basic information

Entry
Database: PDB / ID: 2vl2
TitleOxidized and reduced forms of human peroxiredoxin 5
Components(PEROXIREDOXIN-5) x 2
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 transcription by RNA polymerase III / negative regulation of oxidoreductase activity / NADPH oxidation / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / antioxidant activity ...peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of transcription by RNA polymerase III / negative regulation of oxidoreductase activity / NADPH oxidation / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / antioxidant activity / Detoxification of Reactive Oxygen Species / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / peroxisomal matrix / positive regulation of collagen biosynthetic process / cell redox homeostasis / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / peroxidase activity / cellular response to reactive oxygen species / peroxisome / cellular response to oxidative stress / cytoplasmic vesicle / response to oxidative stress / 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 / cytosol / cytoplasm
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
BENZOIC ACID / Peroxiredoxin-5, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.925 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 8, 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: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain ..._diffrn_source.pdbx_synchrotron_site / _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 1.4Jul 10, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEROXIREDOXIN-5
B: PEROXIREDOXIN-5
C: PEROXIREDOXIN-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8585
Polymers54,6143
Non-polymers2442
Water7,026390
1
A: PEROXIREDOXIN-5
hetero molecules

A: PEROXIREDOXIN-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6644
Polymers36,4202
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1830 Å2
ΔGint-18 kcal/mol
Surface area15920 Å2
MethodPQS
2
B: PEROXIREDOXIN-5
C: PEROXIREDOXIN-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5263
Polymers36,4042
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-11 kcal/mol
Surface area16810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)79.067, 102.016, 146.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2032-

HOH

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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: 18209.850 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-162
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: 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: 18193.850 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-162
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
#3: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.72 Å3/Da / Density % sol: 54.8 % / Description: NONE
Crystal growpH: 8 / Details: NACL 0.1M TRIS PH 8 0.1M PEG 3350 20%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8156
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 7, 2005 / Details: MIRROR 2 BENT, VERTICALLY FOCUSSING
RadiationMonochromator: SI 111, HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8156 Å / Relative weight: 1
ReflectionResolution: 1.92→57.5 Å / Num. obs: 42806 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 25.57 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 24.6
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HD2

1hd2


Resolution: 1.925→57.5 Å / SU ML: 0.32 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2549 2157 5 %
Rwork0.2048 --
obs0.2074 42806 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.32 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 30.99 Å2
Baniso -1Baniso -2Baniso -3
1-6.3718 Å2-0 Å2-0 Å2
2---1.4406 Å20 Å2
3----4.9312 Å2
Refinement stepCycle: LAST / Resolution: 1.925→57.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 18 390 3986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053660
X-RAY DIFFRACTIONf_angle_d1.0184949
X-RAY DIFFRACTIONf_dihedral_angle_d17.8271337
X-RAY DIFFRACTIONf_chiral_restr0.072571
X-RAY DIFFRACTIONf_plane_restr0.004650

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