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- PDB-1zof: Crystal structure of alkyl hydroperoxide-reductase (AhpC) from He... -

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Basic information

Entry
Database: PDB / ID: 1zof
TitleCrystal structure of alkyl hydroperoxide-reductase (AhpC) from Helicobacter Pylori
Componentsalkyl hydroperoxide-reductase
KeywordsOXIDOREDUCTASE / decamer / toroide-shaped complex
Function / homology
Function and homology information


NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / peroxiredoxin activity / peroxidase activity / cytoplasm
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 / Thioredoxin-like superfamily ...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
Alkyl hydroperoxide reductase C
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsPapinutto, E. / Windle, H.J. / Cendron, L. / Battistutta, R. / Kelleher, D. / Zanotti, G.
Citation
Journal: Biochim.Biophys.Acta / Year: 2005
Title: Crystal structure of alkyl hydroperoxide-reductase (AhpC) from Helicobacter pylori.
Authors: Papinutto, E. / Windle, H.J. / Cendron, L. / Battistutta, R. / Kelleher, D. / Zanotti, G.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: The structure of reduced tryparedoxin peroxidase reveals a decamer and insight into reactivity of 2Cys-peroxiredoxins
Authors: Alphey, M.S. / Bond, C.S. / Tetand, E. / Fairlamb, A.H. / Hunter, W.N.
#2: Journal: J.Bacteriol. / Year: 2001
Title: Essential thioredoxin-dependent peroxiredoxin system from Helicobacter pylori: genetic and kinetic characterization
Authors: Baker, L.M.S. / Raudonikiene, A. / Hoffman, P.S. / Poole, L.B.
#3: Journal: TRENDS BIOCHEM.SCI. / Year: 2003
Title: Structure, mechanism and regulation of peroxiredoxins
Authors: Wood, Z.A. / Schroder, E. / Harris, J.R. / Poole, L.B.
History
DepositionMay 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)222,76710
Polymers222,76710
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24550 Å2
ΔGint-201 kcal/mol
Surface area64900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.860, 138.420, 127.540
Angle α, β, γ (deg.)90.00, 125.70, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a decamer in the asymmetric unit

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Components

#1: Protein
alkyl hydroperoxide-reductase / Thioredoxin reductase / 26 kDa antigen / AhpC


Mass: 22276.652 Da / Num. of mol.: 10 / Mutation: V2L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: tsaA / Plasmid: PBAD-THIO-TOPO / Production host: Escherichia coli (E. coli) / References: UniProt: P56876, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.05 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: sodium acetate, sodium formate, pH 4.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.27 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 17, 2004 / Details: mirrors
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27 Å / Relative weight: 1
ReflectionResolution: 2.95→52.8 Å / Num. all: 57514 / Num. obs: 57514 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 157.9 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 7
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.6 / Num. unique all: 8357 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E2Y

1e2y


Resolution: 2.95→52.8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 737506.01 / 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
Rfree0.26 4704 8.2 %RANDOM
Rwork0.236 ---
all0.236 57499 --
obs0.236 57499 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.6117 Å2 / ksol: 0.369771 e/Å3
Displacement parametersBiso mean: 59.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å21.93 Å2
2--7.54 Å20 Å2
3----9.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 2.95→52.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13705 0 0 65 13770
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.89
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.95→3.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 749 7.8 %
Rwork0.374 8802 -
obs-8357 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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