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- PDB-3mng: wild type human PrxV with DTT bound as a competitive inhibitor -

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Basic information

Entry
Database: PDB / ID: 3mng
Titlewild type human PrxV with DTT bound as a competitive inhibitor
ComponentsPeroxiredoxin-5, mitochondrial
KeywordsOXIDOREDUCTASE / peroxiredoxin / peroxidase / PrxV / substrate analog / DTT
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 / 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 / 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 / Detoxification of Reactive Oxygen Species / antioxidant activity / 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 / 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 / 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
BROMIDE ION / (4S,5S)-1,2-DITHIANE-4,5-DIOL / Peroxiredoxin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body refinement of starting model / Resolution: 1.45 Å
AuthorsHall, A. / Karplus, P.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural Evidence that Peroxiredoxin Catalytic Power Is Based on Transition-State Stabilization.
Authors: Hall, A. / Parsonage, D. / Poole, L.B. / Karplus, P.A.
History
DepositionApr 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,30112
Polymers18,3251
Non-polymers97611
Water5,188288
1
A: Peroxiredoxin-5, mitochondrial
hetero molecules

A: Peroxiredoxin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,60124
Polymers36,6502
Non-polymers1,95122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4860 Å2
ΔGint-23 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.313, 67.313, 123.867
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-1016-

HOH

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Components

#1: Protein Peroxiredoxin-5, mitochondrial / Peroxiredoxin V / Prx-V / Peroxisomal antioxidant enzyme / PLP / Thioredoxin reductase / ...Peroxiredoxin V / 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


Mass: 18325.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACR1, aoeb166, arc1, pmp20, PRDX5, SBBI10 / Plasmid: pQE30-Prx5 / Production host: Escherichia coli (E. coli) / Strain (production host): B834/pREP4 / References: UniProt: P30044, peroxiredoxin
#2: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Reservoir contained 1.6 M ammonium sulfate, 0.1 M sodium citrate, 0.2 M sodium/potassium tartrate. Protein was stored at 0.8 mM with 10 mM DTT., pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 18, 2009
RadiationMonochromator: Single crystal, cylindrically bent Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.45→59 Å / Num. obs: 48609 / % possible obs: 99.98 % / Redundancy: 36.7 % / Rsym value: 0.094 / Net I/σ(I): 30.9
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 14 % / Mean I/σ(I) obs: 6.9 / Num. unique all: 7365 / Rsym value: 0.393 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: Rigid body refinement of starting model
Starting model: pdb code 1HD2 with benzoate removed

1hd2


Resolution: 1.45→59 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.923 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13618 2633 5.1 %RANDOM
Rwork0.11303 ---
obs0.11422 48609 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.049 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.29 Å2-0 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.45→59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 28 288 1506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221251
X-RAY DIFFRACTIONr_bond_other_d00.02861
X-RAY DIFFRACTIONr_angle_refined_deg2.7261.9971692
X-RAY DIFFRACTIONr_angle_other_deg2.4133.0012118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1045166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52325.31947
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.91115214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.064155
X-RAY DIFFRACTIONr_chiral_restr0.1610.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02228
X-RAY DIFFRACTIONr_mcbond_it3.1041.5804
X-RAY DIFFRACTIONr_mcbond_other1.0811.5334
X-RAY DIFFRACTIONr_mcangle_it4.35721291
X-RAY DIFFRACTIONr_scbond_it6.93447
X-RAY DIFFRACTIONr_scangle_it9.9694.5398
X-RAY DIFFRACTIONr_rigid_bond_restr2.81632112
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 184 -
Rwork0.166 3564 -
obs--99.84 %

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