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- PDB-4xts: Salmonella typhimurium AhpC T43A mutant -

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Basic information

Entry
Database: PDB / ID: 4xts
TitleSalmonella typhimurium AhpC T43A mutant
ComponentsAlkyl hydroperoxide reductase subunit C
KeywordsOXIDOREDUCTASE / peroxiredoxin / FF / PrxI / conformation
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 enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å
AuthorsPerkins, A. / Nelson, K. / Parsonage, D. / Poole, L. / Karplus, P.A.
CitationJournal: Antioxid.Redox Signal. / Year: 2018
Title: Experimentally Dissecting the Origins of Peroxiredoxin Catalysis.
Authors: Nelson, K.J. / Perkins, A. / Van Swearingen, A.E.D. / Hartman, S. / Brereton, A.E. / Parsonage, D. / Salsbury Jr., F.R. / Karplus, P.A. / Poole, L.B.
History
DepositionJan 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
F: Alkyl hydroperoxide reductase subunit C
G: Alkyl hydroperoxide reductase subunit C
H: Alkyl hydroperoxide reductase subunit C
I: Alkyl hydroperoxide reductase subunit C
J: Alkyl hydroperoxide reductase subunit C
K: Alkyl hydroperoxide reductase subunit C
L: Alkyl hydroperoxide reductase subunit C
M: Alkyl hydroperoxide reductase subunit C
N: Alkyl hydroperoxide reductase subunit C
O: Alkyl hydroperoxide reductase subunit C
P: Alkyl hydroperoxide reductase subunit C
Q: Alkyl hydroperoxide reductase subunit C
R: Alkyl hydroperoxide reductase subunit C
S: Alkyl hydroperoxide reductase subunit C
T: Alkyl hydroperoxide reductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,18047
Polymers412,22320
Non-polymers95727
Water7,566420
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
F: Alkyl hydroperoxide reductase subunit C
G: Alkyl hydroperoxide reductase subunit C
H: Alkyl hydroperoxide reductase subunit C
I: Alkyl hydroperoxide reductase subunit C
J: Alkyl hydroperoxide reductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,60824
Polymers206,11210
Non-polymers49614
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18140 Å2
ΔGint-277 kcal/mol
Surface area64520 Å2
MethodPISA
2
K: Alkyl hydroperoxide reductase subunit C
L: Alkyl hydroperoxide reductase subunit C
M: Alkyl hydroperoxide reductase subunit C
N: Alkyl hydroperoxide reductase subunit C
O: Alkyl hydroperoxide reductase subunit C
P: Alkyl hydroperoxide reductase subunit C
Q: Alkyl hydroperoxide reductase subunit C
R: Alkyl hydroperoxide reductase subunit C
S: Alkyl hydroperoxide reductase subunit C
T: Alkyl hydroperoxide reductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,57323
Polymers206,11210
Non-polymers46113
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18090 Å2
ΔGint-261 kcal/mol
Surface area63990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.651, 109.454, 119.037
Angle α, β, γ (deg.)93.33, 110.02, 114.00
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 20611.162 Da / Num. of mol.: 20 / Mutation: T43A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P0A251, peroxiredoxin
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 25% polyethylene glycol 3350, and 0.1 M BIS-TRIS pH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.7→89.5 Å / Num. obs: 118972 / % possible obs: 96.3 % / Redundancy: 3.6 % / Net I/σ(I): 5.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MA9

4ma9


Resolution: 2.704→63.511 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 11879 5 %imported from 4ma9
Rwork0.1899 ---
obs0.1927 237767 95.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.704→63.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25377 0 27 420 25824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01226026
X-RAY DIFFRACTIONf_angle_d1.65535271
X-RAY DIFFRACTIONf_dihedral_angle_d14.659322
X-RAY DIFFRACTIONf_chiral_restr0.0843860
X-RAY DIFFRACTIONf_plane_restr0.014605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7037-2.73450.37653270.31236000X-RAY DIFFRACTION76
2.7345-2.76660.35573520.31547350X-RAY DIFFRACTION93
2.7666-2.80040.41183860.31667296X-RAY DIFFRACTION93
2.8004-2.83580.33123700.29697418X-RAY DIFFRACTION94
2.8358-2.87310.34173900.2957269X-RAY DIFFRACTION93
2.8731-2.91250.36133680.30767416X-RAY DIFFRACTION94
2.9125-2.95410.36453810.30537501X-RAY DIFFRACTION94
2.9541-2.99820.37344220.28527339X-RAY DIFFRACTION95
2.9982-3.04510.34473920.27367609X-RAY DIFFRACTION95
3.0451-3.0950.32984300.26067365X-RAY DIFFRACTION95
3.095-3.14830.30164000.25547553X-RAY DIFFRACTION96
3.1483-3.20560.3063740.25527624X-RAY DIFFRACTION96
3.2056-3.26720.32144060.2547594X-RAY DIFFRACTION97
3.2672-3.33390.32244080.24777630X-RAY DIFFRACTION97
3.3339-3.40640.28594220.22767602X-RAY DIFFRACTION97
3.4064-3.48560.28514030.22127664X-RAY DIFFRACTION97
3.4856-3.57280.28024200.20427688X-RAY DIFFRACTION98
3.5728-3.66940.24264140.19867598X-RAY DIFFRACTION98
3.6694-3.77740.25073560.1957796X-RAY DIFFRACTION98
3.7774-3.89930.23694580.17727616X-RAY DIFFRACTION98
3.8993-4.03860.22033860.16337795X-RAY DIFFRACTION98
4.0386-4.20030.19744040.14717710X-RAY DIFFRACTION98
4.2003-4.39140.18264100.13337683X-RAY DIFFRACTION98
4.3914-4.62290.17864480.1247636X-RAY DIFFRACTION98
4.6229-4.91240.18024160.11727714X-RAY DIFFRACTION98
4.9124-5.29150.17324020.1247638X-RAY DIFFRACTION98
5.2915-5.82370.18554060.13237714X-RAY DIFFRACTION98
5.8237-6.66560.18063480.13977762X-RAY DIFFRACTION98
6.6656-8.39490.1663660.12387756X-RAY DIFFRACTION98
8.3949-63.52830.15774140.13317552X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 116.9394 Å / Origin y: 6.7638 Å / Origin z: 59.3817 Å
111213212223313233
T0.2539 Å20.0004 Å2-0.0156 Å2-0.2396 Å2-0.0082 Å2--0.2871 Å2
L0.1179 °2-0.0375 °20.0136 °2-0.0346 °2-0.0048 °2--0.0655 °2
S0.0191 Å °0.039 Å °0.0005 Å °-0.0081 Å °-0.0285 Å °0.0075 Å °0.0038 Å °0.0066 Å °0.0071 Å °
Refinement TLS groupSelection details: all

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