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- PDB-1we0: Crystal structure of peroxiredoxin (AhpC) from Amphibacillus xylanus -

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Basic information

Entry
Database: PDB / ID: 1we0
TitleCrystal structure of peroxiredoxin (AhpC) from Amphibacillus xylanus
Componentsalkyl hydroperoxide reductase C
KeywordsOXIDOREDUCTASE / Peroxiredoxin / AhpC
Function / homology
Function and homology information


NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / peroxiredoxin activity / peroxidase activity / response to oxidative stress / cytoplasm
Similarity search - Function
Alkyl hydroperoxide reductase subunit C / 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 ...Alkyl hydroperoxide reductase subunit C / 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
AMMONIUM ION / Alkyl hydroperoxide reductase C / Alkyl hydroperoxide reductase C
Similarity search - Component
Biological speciesAmphibacillus xylanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKitano, K. / Kita, A. / Hakoshima, T. / Niimura, Y. / Miki, K.
Citation
Journal: Proteins / Year: 2005
Title: Crystal structure of decameric peroxiredoxin (AhpC) from Amphibacillus xylanus
Authors: Kitano, K. / Kita, A. / Hakoshima, T. / Niimura, Y. / Miki, K.
#1: Journal: J.Biochem.(Tokyo) / Year: 1999
Title: Stimulation of peroxidase activity by decamerization related to ionic strength: AhpC protein from Amphibacillus xylanus
Authors: Kitano, K. / Niimura, Y. / Nishiyama, Y. / Miki, K.
History
DepositionMay 21, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alkyl hydroperoxide reductase C
B: alkyl hydroperoxide reductase C
C: alkyl hydroperoxide reductase C
D: alkyl hydroperoxide reductase C
E: alkyl hydroperoxide reductase C
F: alkyl hydroperoxide reductase C
G: alkyl hydroperoxide reductase C
H: alkyl hydroperoxide reductase C
I: alkyl hydroperoxide reductase C
J: alkyl hydroperoxide reductase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,66712
Polymers206,63110
Non-polymers362
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.216, 79.319, 104.449
Angle α, β, γ (deg.)77.22, 82.33, 80.08
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a decamer in the asymmetric unit

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Components

#1: Protein
alkyl hydroperoxide reductase C / Peroxiredoxin / AhpC


Mass: 20663.092 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphibacillus xylanus (bacteria) / Plasmid: pAHNO2.5 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: O87200, UniProt: K0J4Q8*PLUS, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 6000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12901
22901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
SYNCHROTRONPhoton Factory BL-18B21
Detector
TypeIDDetector
FUJI1IMAGE PLATE
FUJI2IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 46092 / % possible obs: 83.6 % / Observed criterion σ(I): 12.5
Reflection shellResolution: 2.9→3 Å / % possible all: 55.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / σ(F): 1
RfactorNum. reflection
Rfree0.235 4581
Rwork0.208 -
obs-45388
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12980 0 2 0 12982

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