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- PDB-1qxh: Crystal Structure of Escherichia coli Thiol Peroxidase in the Oxi... -

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Basic information

Entry
Database: PDB / ID: 1qxh
TitleCrystal Structure of Escherichia coli Thiol Peroxidase in the Oxidized State
ComponentsThiol peroxidase
KeywordsOXIDOREDUCTASE / thiol peroxidase / scavengase P20 / antioxidant enzyme / peroxiredoxin
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsChoi, J. / Choi, S. / Choi, J. / Shin, W.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of Escherichia coli thiol peroxidase in the oxidized state: insights into intramolecular disulfide formation and substrate binding in atypical 2-Cys peroxiredoxins
Authors: Choi, J. / Choi, S. / Choi, J. / Cha, M.-K. / Kim, I.-H. / Shin, W.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003
Title: Crystallization and preliminary X-ray analysis of Escherichia coli p20, a novel thiol peroxidase
Authors: Choi, J. / Choi, S. / Choi, J. / Cha, M.-K. / Kim, I.-H. / Shin, W.
History
DepositionSep 6, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)35,4342
Polymers35,4342
Non-polymers00
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.654, 58.428, 127.686
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
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P0A862, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 1.85 Å3/Da / Density % sol: 33.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, iso-propyl alcohol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %PEG40001reservoir
220 %2-propyl alcohol1reservoir
350 mMsodium HEPES1reservoirpH7.
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 8, 2002
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 15120 / Num. obs: 15120 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 16.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 8.5 / Num. unique all: 1429 / Rsym value: 0.21 / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 51963
Reflection shell
*PLUS
% possible obs: 99.4 % / Num. unique obs: 1429 / Num. measured obs: 4891 / Rmerge(I) obs: 0.21

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→20.02 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 930183.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 720 4.9 %RANDOM
Rwork0.191 ---
all0.194 14619 --
obs0.191 14618 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.5007 Å2 / ksol: 0.332231 e/Å3
Displacement parametersBiso mean: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.34 Å20 Å20 Å2
2--3.78 Å20 Å2
3----10.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.2→20.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 0 335 2783
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 94 4.2 %
Rwork0.214 2168 -
obs--90.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Rfactor obs: 0.188 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shell
*PLUS
Rfactor Rfree: 0.28

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