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- PDB-1hd2: Human peroxiredoxin 5 -

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Basic information

Entry
Database: PDB / ID: 1hd2
TitleHuman peroxiredoxin 5
ComponentsPEROXIREDOXIN 5 RESIDUES 54-214
KeywordsANTIOXIDANT ENZYME / PEROXIREDOXIN / THIOREDOXIN PEROXIDASE / 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 / cellular response to oxidative stress / 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
BENZOIC ACID / BROMIDE ION / Peroxiredoxin-5, mitochondrial / Peroxiredoxin-5, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsDeclercq, J.P. / Evrard, C.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of Human Peroxiredoxin 5, a Novel Type of Mammalian Peroxiredoxin at 1.5 A Resolution.
Authors: Declercq, J.P. / Evrard, C. / Clippe, A. / Stricht, D.V. / Bernard, A. / Knoops, B.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Cloning and Characterization of Aoeb166, a Novel Mammalian Antioxidant Enzyme of the Peroxiredoxin Family
Authors: Knoops, B. / Clippe, A. / Bogard, C. / Arsalane, K. / Wattiez, R. / Hermans, C. / Duconseille, E. / Falmagne, P. / Bernard, A.
History
DepositionNov 6, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 4, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details ..._pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.5May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: KABSCH AND SANDER
Remark 700 SHEET DETERMINATION METHOD: KABSCH AND SANDER

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEROXIREDOXIN 5 RESIDUES 54-214
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4417
Polymers16,9201
Non-polymers5226
Water3,981221
1
A: PEROXIREDOXIN 5 RESIDUES 54-214
hetero molecules

A: PEROXIREDOXIN 5 RESIDUES 54-214
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,88214
Polymers33,8392
Non-polymers1,04312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3310 Å2
ΔGint-8 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.607, 66.607, 123.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2057-

HOH

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Components

#1: Protein PEROXIREDOXIN 5 RESIDUES 54-214 / PRDX5 / PRXV / AOEB166 / PMP20 / ARC1


Mass: 16919.514 Da / Num. of mol.: 1 / Fragment: RESIDUES 54-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: MITOCHONDRIA-CYTOSOL-PEROXISOME / Gene: PRDX5, AOEB166, PMP20, ARC1 / Organ: LUNG / Organelle: MITOCHONDRIA-CYTOSOL-PEROXISOME / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: Q9UKX4, UniProt: P30044*PLUS
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growpH: 5.3
Details: PROTEIN WAS CRYSTALLIZED FROM 1.6 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE BUFFER PH 5.3, 0.2 M POTASSIUM SODIUM TARTRATE, 1 MM DTT, 0.02 % (W/V) SODIUM AZIDE
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.6 Mammonium sulfate1reservoir
30.1 Msodium citrate1reservoir
40.2 Mpotassium/sodium tartrate1reservoir
50.001 M1,4-dithio-DL-threitol1reservoir
60.02 %(w/v)sodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.1,0.9175,0.9169,0.855
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 15, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.91751
30.91691
40.8551
ReflectionResolution: 1.5→16 Å / Num. obs: 45181 / % possible obs: 100 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 24
Reflection shellResolution: 1.5→1.72 Å / Redundancy: 8 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 7 / Rsym value: 0.246 / % possible all: 100
Reflection
*PLUS
Num. measured all: 384543

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→16 Å / Num. parameters: 12850 / Num. restraintsaints: 15197 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.037
RfactorNum. reflection% reflectionSelection details
Rfree0.1645 2256 5 %RANDOM
all0.1332 45181 --
obs0.1325 -100 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 1059 / Occupancy sum non hydrogen: 1424.5
Refinement stepCycle: LAST / Resolution: 1.5→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 14 221 1425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0281
X-RAY DIFFRACTIONs_zero_chiral_vol0.075
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.075
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.043
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.058
X-RAY DIFFRACTIONs_approx_iso_adps0.103
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.1325
Solvent computation
*PLUS
Displacement parameters
*PLUS

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