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- PDB-3emp: Crystal Structure of the S-acetanilide modified form of C165S AhpC -

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Basic information

Entry
Database: PDB / ID: 3emp
TitleCrystal Structure of the S-acetanilide modified form of C165S AhpC
ComponentsAlkyl hydroperoxide reductase subunit C
KeywordsOXIDOREDUCTASE / AhpC / peroxiredoxin / Antioxidant / Peroxidase / Redox-active center
Function / homology
Function and homology information


NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / cytosol
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 ...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
Alkyl hydroperoxide reductase C
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4 Å
AuthorsKarplus, P.A. / Hall, A.
CitationJournal: Biochemistry / Year: 2008
Title: Cysteine pK(a) Values for the Bacterial Peroxiredoxin AhpC
Authors: Nelson, K.J. / Parsonage, D. / Hall, A. / Karplus, P.A. / Poole, L.B.
History
DepositionSep 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
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 1.4Sep 6, 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 subunit C
B: Alkyl hydroperoxide reductase subunit C
C: Alkyl hydroperoxide reductase subunit C
D: Alkyl hydroperoxide reductase subunit C
E: Alkyl hydroperoxide reductase subunit C


Theoretical massNumber of molelcules
Total (without water)103,1265
Polymers103,1265
Non-polymers00
Water00
1
A: Alkyl hydroperoxide reductase subunit C
B: Alkyl hydroperoxide reductase subunit C
C: Alkyl hydroperoxide reductase subunit C
D: Alkyl hydroperoxide reductase subunit C
E: Alkyl hydroperoxide reductase subunit C

A: Alkyl hydroperoxide reductase subunit C
B: Alkyl hydroperoxide reductase subunit C
C: Alkyl hydroperoxide reductase subunit C
D: Alkyl hydroperoxide reductase subunit C
E: Alkyl hydroperoxide reductase subunit C


Theoretical massNumber of molelcules
Total (without water)206,25110
Polymers206,25110
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area16380 Å2
ΔGint-114 kcal/mol
Surface area64510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.315, 137.315, 145.805
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Alkyl hydroperoxide reductase subunit C / Peroxiredoxin / Thioredoxin peroxidase / Alkyl hydroperoxide reductase protein C22


Mass: 20625.123 Da / Num. of mol.: 5 / Mutation: C165S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: ahpC / Plasmid: PAC1 / Production host: Escherichia coli (E. coli) / Strain (production host): TA4315 / References: UniProt: P0A251, 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: 3.84 Å3/Da / Density % sol: 68.01 %
Crystal growTemperature: 277 K / pH: 6
Details: 1.26 M (NH4)2SO4, 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 17, 2006
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 4→100 Å / Num. obs: 13761 / % possible obs: 98.4 %
Reflection shellResolution: 4→4.14 Å / Rmerge(I) obs: 0.508 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
DMphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YF1

1yf1


Resolution: 4→17.06 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.861 / Occupancy max: 1 / Occupancy min: 1 / SU B: 0.006 / SU ML: 0 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.309 685 5 %RANDOM
Rwork0.301 ---
obs0.302 12924 98.4 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 45.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.46 Å2-0 Å2
2--0.93 Å2-0 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 4→17.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6379 0 0 0 6379
LS refinement shellResolution: 4→4.1 Å
RfactorNum. reflection% reflection
Rfree0.396 64 -
Rwork0.394 947 -
obs--100 %

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