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- PDB-4k7i: HUMAN PEROXIREDOXIN 5 with a fragment -

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Basic information

Entry
Database: PDB / ID: 4k7i
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 / 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 transcription by RNA polymerase III / negative regulation of oxidoreductase activity / 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 / TP53 Regulates Metabolic Genes / hydrogen peroxide catabolic process / cellular response to reactive oxygen species / peroxidase activity / peroxisome / response to oxidative stress / cellular response to oxidative stress / cytoplasmic vesicle / mitochondrial matrix / inflammatory response / intracellular membrane-bounded organelle / signaling receptor binding / 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
CATECHOL / Peroxiredoxin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)53,8837
Polymers53,5063
Non-polymers3764
Water6,882382
1
A: Peroxiredoxin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0243
Polymers17,8351
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxiredoxin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0243
Polymers17,8351
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peroxiredoxin-5, mitochondrial


Theoretical massNumber of molelcules
Total (without water)17,8351
Polymers17,8351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Peroxiredoxin-5, mitochondrial
hetero molecules

A: Peroxiredoxin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0476
Polymers35,6712
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1500 Å2
ΔGint-13 kcal/mol
Surface area13230 Å2
MethodPISA
5
B: Peroxiredoxin-5, mitochondrial
C: Peroxiredoxin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8594
Polymers35,6712
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-13 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.599, 103.762, 144.935
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-2139-

HOH

21C-319-

HOH

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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: catalytic domain, 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-CAQ / CATECHOL / 1,2-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56.02 %
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: ID14-4 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2012
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.25→47.6 Å / Num. all: 29176 / Num. obs: 28855 / % possible obs: 98.9 % / Observed criterion σ(F): 5.3 / Observed criterion σ(I): 2.1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.09
Reflection shellResolution: 2.25→47.6 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 5.3 / % possible all: 98.9

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Processing

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

1hd2


Resolution: 2.25→47.6 Å / Cross valid method: THROUGHOUT / σ(F): 2.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22489 1442 5.1 %RANDOM
Rwork0.17467 ---
all-29176 --
obs-27007 --
Displacement parametersBiso mean: 27.986 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2--0.16 Å2-0 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 24 382 3974

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