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- PDB-3w6g: Structure of peroxiredoxin from anaerobic hyperthermophilic archa... -

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Basic information

Entry
Database: PDB / ID: 3w6g
TitleStructure of peroxiredoxin from anaerobic hyperthermophilic archaeon Pyrococcus horikoshii
ComponentsProbable peroxiredoxin
KeywordsOXIDOREDUCTASE / Reduction / hydrogen peroxide / water
Function / homology
Function and homology information


cellular response to stress / thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / cellular response to oxygen levels / thioredoxin peroxidase activity / antioxidant activity / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / cytosol
Similarity search - Function
Antioxidant, Horf6; Chain A, domain 2 / Antioxidant, Horf6; Chain A, domain2 / Peroxiredoxin, TDXH subfamily / 1-Cys peroxiredoxin / 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. ...Antioxidant, Horf6; Chain A, domain 2 / Antioxidant, Horf6; Chain A, domain2 / Peroxiredoxin, TDXH subfamily / 1-Cys peroxiredoxin / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Peroxiredoxin
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsNakamura, T. / Mori, A. / Niiyama, M. / Matsumura, H. / Tokuyama, C. / Morita, J. / Uegaki, K. / Inoue, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of peroxiredoxin from the anaerobic hyperthermophilic archaeon Pyrococcus horikoshii
Authors: Nakamura, T. / Mori, A. / Niiyama, M. / Matsumura, H. / Tokuyama, C. / Morita, J. / Uegaki, K. / Inoue, T.
History
DepositionFeb 14, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable peroxiredoxin
B: Probable peroxiredoxin
C: Probable peroxiredoxin
D: Probable peroxiredoxin
E: Probable peroxiredoxin
F: Probable peroxiredoxin
G: Probable peroxiredoxin
H: Probable peroxiredoxin
I: Probable peroxiredoxin
J: Probable peroxiredoxin
K: Probable peroxiredoxin
L: Probable peroxiredoxin
M: Probable peroxiredoxin
N: Probable peroxiredoxin
O: Probable peroxiredoxin
P: Probable peroxiredoxin
Q: Probable peroxiredoxin
R: Probable peroxiredoxin
S: Probable peroxiredoxin
T: Probable peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)499,59640
Polymers495,81420
Non-polymers3,78220
Water18,4831026
1
A: Probable peroxiredoxin
B: Probable peroxiredoxin
C: Probable peroxiredoxin
D: Probable peroxiredoxin
E: Probable peroxiredoxin
F: Probable peroxiredoxin
G: Probable peroxiredoxin
H: Probable peroxiredoxin
I: Probable peroxiredoxin
J: Probable peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,79820
Polymers247,90710
Non-polymers1,89110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44720 Å2
ΔGint-244 kcal/mol
Surface area71860 Å2
MethodPISA
2
K: Probable peroxiredoxin
L: Probable peroxiredoxin
M: Probable peroxiredoxin
N: Probable peroxiredoxin
O: Probable peroxiredoxin
P: Probable peroxiredoxin
Q: Probable peroxiredoxin
R: Probable peroxiredoxin
S: Probable peroxiredoxin
T: Probable peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,79820
Polymers247,90710
Non-polymers1,89110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44780 Å2
ΔGint-250 kcal/mol
Surface area70840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.354, 94.733, 228.204
Angle α, β, γ (deg.)90.00, 103.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable peroxiredoxin


Mass: 24790.695 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1217 / Production host: Escherichia coli (E. coli) / References: UniProt: O58966, peroxiredoxin
#2: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1026 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1 M Na-citrate, 20% PEG 3350, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 9, 2012
RadiationMonochromator: douvle-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 245717 / Num. obs: 233950 / % possible obs: 95.2 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 5.4 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.1
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 4.7 / Num. unique all: 21838 / % possible all: 89.5

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→43.57 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.237 11674 Random
Rwork0.198 --
obs0.198 233921 -
all-245717 -
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0.19 Å2
2---0.05 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.25→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34640 0 260 1026 35926
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.006
RfactorNum. reflection% reflection
Rfree0.266 1758 -
Rwork0.232 --
obs-34049 87.6 %

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