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- PDB-3zvj: Crystal structure of high molecular weight (HMW) form of Peroxire... -

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Basic information

Entry
Database: PDB / ID: 3zvj
TitleCrystal structure of high molecular weight (HMW) form of Peroxiredoxin I from Schistosoma mansoni
Components(THIOREDOXIN PEROXIDASE) x 2
KeywordsOXIDOREDUCTASE / SCHISTOSOMIASIS / CHAPERONE / THIOREDOXIN FOLD
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cellular response to stress / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / identical protein binding / cytosol
Similarity search - Function
Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin peroxidase
Similarity search - Component
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSaccoccia, F. / Angelucci, F. / Bellelli, A. / Boumis, G. / Brunori, M. / Miele, A.E.
CitationJournal: Structure / Year: 2012
Title: Moonlighting by Different Stressors: Crystal Structure of the Chaperone Species of a 2-Cys Peroxiredoxin.
Authors: Saccoccia, F. / Di Micco, P. / Boumis, G. / Brunori, M. / Koutris, I. / Miele, A.E. / Morea, V. / Sriratana, P. / Williams, D.L. / Bellelli, A. / Angelucci, F.
History
DepositionJul 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOREDOXIN PEROXIDASE
B: THIOREDOXIN PEROXIDASE
C: THIOREDOXIN PEROXIDASE
D: THIOREDOXIN PEROXIDASE
E: THIOREDOXIN PEROXIDASE
F: THIOREDOXIN PEROXIDASE
G: THIOREDOXIN PEROXIDASE
H: THIOREDOXIN PEROXIDASE
I: THIOREDOXIN PEROXIDASE
J: THIOREDOXIN PEROXIDASE
K: THIOREDOXIN PEROXIDASE
L: THIOREDOXIN PEROXIDASE
M: THIOREDOXIN PEROXIDASE
N: THIOREDOXIN PEROXIDASE
O: THIOREDOXIN PEROXIDASE
P: THIOREDOXIN PEROXIDASE
Q: THIOREDOXIN PEROXIDASE
R: THIOREDOXIN PEROXIDASE
S: THIOREDOXIN PEROXIDASE
T: THIOREDOXIN PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)497,04220
Polymers497,04220
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50170 Å2
ΔGint-334.1 kcal/mol
Surface area164110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.911, 204.940, 126.845
Angle α, β, γ (deg.)90.00, 114.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
THIOREDOXIN PEROXIDASE / PEROXIREDOXIN 1 / THIOREDOXIN PEROXIDASE 1


Mass: 24852.109 Da / Num. of mol.: 19
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PRSETA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR(DE3) / Variant (production host): PLYSS / References: UniProt: O97161, peroxiredoxin
#2: Protein THIOREDOXIN PEROXIDASE / PEROXIREDOXIN 1 / THIOREDOXIN PEROXIDASE 1


Mass: 24852.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PRSETA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR(DE3)PLYSS / References: UniProt: O97161, peroxiredoxin

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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: 3.7 Å3/Da / Density % sol: 66.81 %
Description: PERFECT PSEUDOMEROHEDRALLY TWINNED CRYSTAL. THE TWINNING WAS TAKEN INTO ACCOUNT AND IT WAS OVERCOME ONLY DURING REFINEMENT STEPS, NOT DURING DATA REDUCTION.
Crystal growpH: 4.2
Details: 20% PEG 8000, 0.2M SODIUM CHLORIDE, 0.1M PHOSPHATE-CITRATE, PH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
Reflection twinOperator: L,-K,H / Fraction: 0.5
ReflectionResolution: 3→29.86 Å / Num. obs: 112406 / % possible obs: 95.7 % / Observed criterion σ(I): -1 / Redundancy: 3.6 % / Biso Wilson estimate: 13.03 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 6.14
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.85 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZTL

3ztl


Resolution: 3→29.857 Å / σ(F): 2.2 / Phase error: 23.91 / Stereochemistry target values: TWIN_LSQ_F
Details: PERFECT PSEUDOMEROHEDRALLY TWINNED CRYSTAL. THE TWINNING WAS TAKEN INTO ACCOUNT AND IT WAS OVERCOME ONLY DURING REFINEMENT STEPS, NOT DURING DATA REDUCTION. PERFECT PSEUDOMEROHEDRALLY ...Details: PERFECT PSEUDOMEROHEDRALLY TWINNED CRYSTAL. THE TWINNING WAS TAKEN INTO ACCOUNT AND IT WAS OVERCOME ONLY DURING REFINEMENT STEPS, NOT DURING DATA REDUCTION. PERFECT PSEUDOMEROHEDRALLY TWINNED CRYSTAL. THE TWINNING WAS TAKEN INTO ACCOUNT AND IT WAS OVERCOME ONLY DURING REFINEMENT STEPS, NOT DURING DATA REDUCTION.
RfactorNum. reflection% reflection
Rfree0.2695 5845 5.2 %
Rwork0.2191 --
obs0.2328 112406 95.69 %
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.001 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso mean: 40.427 Å2
Baniso -1Baniso -2Baniso -3
1--19.4053 Å20 Å24.1235 Å2
2---8.256 Å20 Å2
3----15.4632 Å2
Refinement stepCycle: LAST / Resolution: 3→29.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26988 0 0 0 26988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727597
X-RAY DIFFRACTIONf_angle_d0.99437281
X-RAY DIFFRACTIONf_dihedral_angle_d14.06710255
X-RAY DIFFRACTIONf_chiral_restr0.074004
X-RAY DIFFRACTIONf_plane_restr0.0054938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0029-3.05470.3132810.21674946X-RAY DIFFRACTION85
3.0547-3.11020.31712500.21225130X-RAY DIFFRACTION88
3.1102-3.16990.31522850.2225213X-RAY DIFFRACTION89
3.1699-3.23460.28832800.21915135X-RAY DIFFRACTION89
3.2346-3.30480.27632780.21445250X-RAY DIFFRACTION90
3.3048-3.38160.28832520.21075286X-RAY DIFFRACTION91
3.3816-3.4660.28522890.20135313X-RAY DIFFRACTION91
3.466-3.55960.26042850.19945413X-RAY DIFFRACTION92
3.5596-3.66410.27133110.21925333X-RAY DIFFRACTION91
3.6641-3.78220.26392860.21235347X-RAY DIFFRACTION92
3.7822-3.91710.2722640.21095451X-RAY DIFFRACTION93
3.9171-4.07360.29152920.21725446X-RAY DIFFRACTION93
4.0736-4.25850.29472860.24995310X-RAY DIFFRACTION91
4.2585-4.48230.28273030.2415445X-RAY DIFFRACTION92
4.4823-4.7620.28793000.23815408X-RAY DIFFRACTION93
4.762-5.1280.3092810.26535431X-RAY DIFFRACTION93
5.128-5.64090.34162670.29825441X-RAY DIFFRACTION93
5.6409-6.450.35992670.29295466X-RAY DIFFRACTION93
6.45-8.09940.29972840.29865384X-RAY DIFFRACTION91
8.0994-29.85810.21042860.18085582X-RAY DIFFRACTION94

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