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- PDB-4owy: Crystal Structure of Ahp1 from Saccharomyces cerevisiae. Investig... -

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Basic information

Entry
Database: PDB / ID: 4owy
TitleCrystal Structure of Ahp1 from Saccharomyces cerevisiae. Investigating the electron transfers.
ComponentsPeroxiredoxin type-2
KeywordsOXIDOREDUCTASE / Peroxiredoxin / Ahp1 / Electron Transfer
Function / homology
Function and homology information


TP53 Regulates Metabolic Genes / Detoxification of Reactive Oxygen Species / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / response to metal ion / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / cellular response to oxidative stress / mitochondrion ...TP53 Regulates Metabolic Genes / Detoxification of Reactive Oxygen Species / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / response to metal ion / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / cellular response to oxidative stress / mitochondrion / plasma membrane / 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
ACETIC ACID / DI(HYDROXYETHYL)ETHER / TERTIARY-BUTYL ALCOHOL / Peroxiredoxin AHP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsSchultz, L. / Genu, V. / Breyer, C.A. / dos Santos, V.F. / Guimaraes, B.G. / Netto, L.E.S. / de Oliveira, M.A.
CitationJournal: To be published
Title: Crystal Structure of Ahp1 from Saccharomyces cerevisiae. Investigating the electron transfers.
Authors: Schultz, L. / Genu, V. / Breyer, C.A. / dos Santos, V.F. / Guimaraes, B.G. / de Oliveira, M.A. / Netto, L.E.S.
History
DepositionFeb 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin type-2
B: Peroxiredoxin type-2
C: Peroxiredoxin type-2
D: Peroxiredoxin type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,95513
Polymers85,2164
Non-polymers7399
Water2,360131
1
A: Peroxiredoxin type-2
B: Peroxiredoxin type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0927
Polymers42,6082
Non-polymers4855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-12 kcal/mol
Surface area14270 Å2
MethodPISA
2
C: Peroxiredoxin type-2
D: Peroxiredoxin type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8626
Polymers42,6082
Non-polymers2544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-18 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.127, 127.799, 66.421
Angle α, β, γ (deg.)90.00, 103.24, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 176
2114B1 - 176
3114C1 - 176
4114D1 - 176

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.891276, -0.068936, 0.448192), (-0.065638, -0.99758, -0.02291), (0.448687, -0.008999, -0.893644)-12.37758, 2.47162, 52.2932
3given(-0.999753, 0.0199, 0.00993), (-0.019661, -0.999528, 0.023611), (0.010395, 0.02341, 0.999672)3.17891, 35.03872, -0.65915
4given(-0.882856, 0.078735, 0.462996), (0.069863, 0.996896, -0.03631), (-0.464418, 0.00029, -0.885616)-11.79018, -32.84501, 53.71629

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Components

#1: Protein
Peroxiredoxin type-2 / AHPC1 / Cytoplasmic thiol peroxidase 3 / cTPx 3 / Peroxiredoxin type II / Peroxisomal alkyl ...AHPC1 / Cytoplasmic thiol peroxidase 3 / cTPx 3 / Peroxiredoxin type II / Peroxisomal alkyl hydroperoxide reductase / TPx type II / Thiol-specific antioxidant II / TSA II / Thioredoxin peroxidase type II / Thioredoxin reductase type II


Mass: 21303.971 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: BY4741 / Gene: AHP1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P38013, peroxiredoxin
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36.13 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG 3000, 0.2M CaAc and 0.1M Bis-Tris Propane

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.421 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 14, 2007
RadiationMonochromator: Single Crystal Monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.421 Å / Relative weight: 1
ReflectionResolution: 2.2→42.64 Å / Num. obs: 32233 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.1
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.416 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementResolution: 2.2→42.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.924 / SU B: 13.593 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1631 5.1 %RANDOM
Rwork0.18 ---
obs0.184 30573 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5109 0 45 131 5285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.025270
X-RAY DIFFRACTIONr_bond_other_d0.0020.024919
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.9367201
X-RAY DIFFRACTIONr_angle_other_deg0.8243.00111288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0755680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.40525.464194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78415758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.808154
X-RAY DIFFRACTIONr_chiral_restr0.1210.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215988
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021128
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2234 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.40.5
2Bmedium positional0.360.5
3Cmedium positional0.40.5
4Dmedium positional0.340.5
1Amedium thermal4.192
2Bmedium thermal4.962
3Cmedium thermal7.552
4Dmedium thermal4.812
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 119 -
Rwork0.26 2233 -
obs--100 %

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