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- PDB-3i43: Escherichia coli Thiol peroxidase (Tpx) wild type disulfide form -

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Basic information

Entry
Database: PDB / ID: 3i43
TitleEscherichia coli Thiol peroxidase (Tpx) wild type disulfide form
ComponentsThiol peroxidase
KeywordsOXIDOREDUCTASE / TPX / PEROXIREDOXIN / PEROXIDASE / ANTIOXIDANT
Function / homology
Function and homology information


hydroperoxide reductase activity / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cellular response to oxidative stress / periplasmic space / cytosol
Similarity search - Function
Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Thiol peroxidase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / Difference fourier based on isomorphous starting model / Resolution: 2.8 Å
AuthorsHall, A. / Karplus, P.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural changes common to catalysis in the Tpx peroxiredoxin subfamily.
Authors: Hall, A. / Sankaran, B. / Poole, L.B. / Karplus, P.A.
History
DepositionJul 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 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: Thiol peroxidase
B: Thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8184
Polymers35,4342
Non-polymers3842
Water10,845602
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-2 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.830, 64.000, 137.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thiol peroxidase / Scavengase P20


Mass: 17717.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: See Baker and Poole, 2003. / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 (XL-1 Blue) / Gene: b1324, JW1317, tpx, yzzJ / Plasmid: pPROK1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 Blue / References: UniProt: P0A862, peroxiredoxin
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 20% (w/v) PEG-8000, 0.1 M phosphate citrate, 0.2 M sodium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 28, 2008 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.8→37.36 Å / Num. obs: 7832 / % possible obs: 96.88 % / Redundancy: 2.9 % / Rsym value: 0.105 / Net I/σ(I): 7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1267 / Rsym value: 0.368 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.5.0046refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: Difference fourier based on isomorphous starting model
Starting model: PDB ENTRY 3HVS

3hvs


Resolution: 2.8→37.36 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.91 / SU B: 0.005 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: This is not a stand alone structure, but is derived from the higher resolution structure 3HVS by a simple rigid body refinement combined with manual adjustment and geometry optimization of ...Details: This is not a stand alone structure, but is derived from the higher resolution structure 3HVS by a simple rigid body refinement combined with manual adjustment and geometry optimization of only the catalytic residues Cys61 and Cys95. This data set is at much lower resolution and was only used to confirm the presence of an intact disulfide. The conformation of Cys61 and Cys95 from this structure has been added as an alternate conformation with zero occupancy to the higher resolution structure 3HVS and we recommend use of that structure rather than this one.
RfactorNum. reflection% reflectionSelection details
Rfree0.21931 849 9.8 %RANDOM
Rwork0.19819 ---
obs0.20029 7832 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å2-0 Å2
2---1.7 Å2-0 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.8→37.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 26 602 3122
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 68 -
Rwork0.308 543 -
obs--98.87 %

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