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- PDB-4k7n: HUMAN PEROXIREDOXIN 5 with a fragment -

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Basic information

Entry
Database: PDB / ID: 4k7n
TitleHUMAN PEROXIREDOXIN 5 with a fragment
ComponentsPeroxiredoxin-5, mitochondrial
KeywordsOXIDOREDUCTASE / enzyme / cytosol
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
4-METHYLCATECHOL / Peroxiredoxin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGuichou, J.F.
CitationJournal: Plos One / Year: 2014
Title: Comparing Binding Modes of Analogous Fragments Using NMR in Fragment-Based Drug Design: Application to PRDX5
Authors: Aguirre, C. / Brink, T.T. / Guichou, J.F. / Cala, O. / Krimm, I.
History
DepositionApr 17, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Peroxiredoxin-5, mitochondrial
B: Peroxiredoxin-5, mitochondrial
C: Peroxiredoxin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8796
Polymers53,5063
Non-polymers3723
Water2,630146
1
A: Peroxiredoxin-5, mitochondrial
hetero molecules

A: Peroxiredoxin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9194
Polymers35,6712
Non-polymers2482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area1520 Å2
ΔGint-13 kcal/mol
Surface area13220 Å2
MethodPISA
2
B: Peroxiredoxin-5, mitochondrial
C: Peroxiredoxin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9194
Polymers35,6712
Non-polymers2482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-13 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.115, 101.527, 155.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Peroxiredoxin-5, mitochondrial / / Alu corepressor 1 / Antioxidant enzyme B166 / AOEB166 / Liver tissue 2D-page spot 71B / PLP / ...Alu corepressor 1 / Antioxidant enzyme B166 / AOEB166 / Liver tissue 2D-page spot 71B / PLP / Peroxiredoxin V / Prx-V / Peroxisomal antioxidant enzyme / TPx type VI / Thioredoxin peroxidase PMP20 / Thioredoxin reductase


Mass: 17835.475 Da / Num. of mol.: 3 / Fragment: UNP residues 54-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX5, ACR1, SBBI10 / Production host: Escherichia coli (E. coli) / References: UniProt: P30044, peroxiredoxin
#2: Chemical ChemComp-MCT / 4-METHYLCATECHOL / 4-METHYL-1,2-BENZENEDIOL / 4-Methylcatechol


Mass: 124.137 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 22% PEG3350, 0.1M sodium citrate buffer, 0.2M potassium sodium tartrate, 5mM 1,4-dithio-dl-threitol, 0.02%(w/v) sodium azide, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2013
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.3→48.9 Å / Num. all: 27075 / Num. obs: 26994 / % possible obs: 99.7 % / Observed criterion σ(F): 9.1 / Observed criterion σ(I): 1.9 / Redundancy: 5.7 % / Rmerge(I) obs: 0.057
Reflection shellResolution: 2.3→48.9 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 9.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
DNAdata collection
AMoREphasing
REFMAC5.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HD2

1hd2


Resolution: 2.3→48.9 Å / Cross valid method: THROUGHOUT / σ(F): 9.1 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23211 1438 5.1 %RANDOM
Rwork0.18758 ---
all-27075 --
obs-26994 --
Displacement parametersBiso mean: 45.893 Å2
Baniso -1Baniso -2Baniso -3
1-3.32 Å20 Å20 Å2
2---2.22 Å2-0 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3570 0 27 146 3743

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