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- PDB-1qq2: CRYSTAL STRUCTURE OF A MAMMALIAN 2-CYS PEROXIREDOXIN, HBP23. -

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Basic information

Entry
Database: PDB / ID: 1qq2
TitleCRYSTAL STRUCTURE OF A MAMMALIAN 2-CYS PEROXIREDOXIN, HBP23.
ComponentsTHIOREDOXIN PEROXIDASE 2
KeywordsOXIDOREDUCTASE / THIOREDOXIN FOLD
Function / homology
Function and homology information


NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / leukocyte activation / TP53 Regulates Metabolic Genes / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / natural killer cell mediated cytotoxicity / thioredoxin peroxidase activity / natural killer cell activation ...NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / leukocyte activation / TP53 Regulates Metabolic Genes / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / natural killer cell mediated cytotoxicity / thioredoxin peroxidase activity / natural killer cell activation / erythrocyte homeostasis / regulation of stress-activated MAPK cascade / peroxisomal matrix / canonical NF-kappaB signal transduction / removal of superoxide radicals / cell redox homeostasis / response to reactive oxygen species / hydrogen peroxide catabolic process / euchromatin / peroxidase activity / fibroblast proliferation / response to oxidative stress / mitochondrial matrix / heme binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsHirotsu, S. / Abe, Y. / Okada, K. / Nagahara, N. / Hori, H. / Nishino, T. / Hakoshima, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of a multifunctional 2-Cys peroxiredoxin heme-binding protein 23 kDa/proliferation-associated gene product.
Authors: Hirotsu, S. / Abe, Y. / Okada, K. / Nagahara, N. / Hori, H. / Nishino, T. / Hakoshima, T.
History
DepositionJun 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN PEROXIDASE 2
B: THIOREDOXIN PEROXIDASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3164
Polymers44,2452
Non-polymers712
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-45 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.900, 73.900, 211.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein THIOREDOXIN PEROXIDASE 2 / HEME-BINDING PROTEIN 23 KD / HBP23


Mass: 22122.338 Da / Num. of mol.: 2 / Mutation: C83S
Source method: isolated from a genetically manipulated source
Details: HBP23 in oxidative form revealed a unique dimer structure in which the active site cystein forms a disulfide bond with other cystein from another subunit.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: CYTOPLASM / Organ: LIVER / Plasmid: PET3C / Production host: Escherichia coli (E. coli) / References: UniProt: Q63716
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, POTASSIUM PHOSPHATE, SODIUM CHLORIDE, CHAPS, pH 6.00, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
220 mMsodium phosphate1drop
31 mMCHAPS1drop
42 M1reservoirNaCl
510 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 28, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 262009 / % possible obs: 88.9 % / Observed criterion σ(I): 0.5 / Redundancy: 8.5 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.335 / % possible all: 72.5
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 40 Å / Observed criterion σ(I): 0.5 / Redundancy: 8.5 % / Biso Wilson estimate: 39.2 Å2
Reflection shell
*PLUS
Redundancy: 2.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
X-PLOR98refinement
RefinementResolution: 2.6→20 Å / σ(F): 1 / Details: USED SLOW-COOLING METHOD WITH BULK SOLVENT MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1952 -RANDOM
Rwork0.216 ---
obs0.216 153566 92.7 %-
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 2 62 2764
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 98 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg26
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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