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- PDB-1yf1: Structural and biochemical analysis of the link between enzymatic... -

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Basic information

Entry
Database: PDB / ID: 1yf1
TitleStructural and biochemical analysis of the link between enzymatic activity and oligomerization in AhpC, a bacterial peroxiredoxin.
ComponentsAlkyl hydroperoxide reductase subunit C
KeywordsOXIDOREDUCTASE / peroxiredoxin / AhpC / Alkyl hydroperoxide reductase subunit C
Function / homology
Function and homology information


NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / cellular response to stress / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsParsonage, D. / Youngblood, D.S. / Sarma, G.N. / Wood, Z.A. / Karplus, P.A. / Poole, L.B.
CitationJournal: Biochemistry / Year: 2005
Title: Analysis of the Link between Enzymatic Activity and Oligomeric State in AhpC, a Bacterial Peroxiredoxin.
Authors: Parsonage, D. / Youngblood, D.S. / Sarma, G.N. / Wood, Z.A. / Karplus, P.A. / Poole, L.B.
History
DepositionDec 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 9, 2012Group: Structure summary
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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: 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)206,41511
Polymers206,39210
Non-polymers231
Water14,880826
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,43812
Polymers206,39210
Non-polymers462
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area18360 Å2
ΔGint-148 kcal/mol
Surface area65600 Å2
MethodPISA, PQS
2
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


Theoretical massNumber of molelcules
Total (without water)103,1965
Polymers103,1965
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18420 Å2
ΔGint-152 kcal/mol
Surface area66150 Å2
MethodPISA
3
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

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


Theoretical massNumber of molelcules
Total (without water)206,39210
Polymers206,39210
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)136.350, 169.960, 117.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-6001-

NA

21F-1501-

HOH

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Components

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


Mass: 20639.215 Da / Num. of mol.: 10 / Mutation: T77V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: ahpC / Production host: Escherichia coli (E. coli) / References: UniProt: P0A251, peroxiredoxin
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 826 / 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: 3.3 Å3/Da / Density % sol: 62.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 3350, citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 31, 2003
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→100 Å / Num. all: 79146 / Num. obs: 79146 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.7 Å / % possible all: 92.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→100 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Waters have been sorted by chain contact and electron density. The water number thousandth place indicates the protein chain it is in contact with (A=1, B=2, etc.) and within each series an ...Details: Waters have been sorted by chain contact and electron density. The water number thousandth place indicates the protein chain it is in contact with (A=1, B=2, etc.) and within each series an increase in number corresponds to a decrease in average peak density of equivalent waters from different chains. The waters in the second pentamer are numbered by adding 500 to the corresponding water in the first pentamer. For instance, water 2005 is in contact with chain B and is equivalent to waters 1005, 3005, 4005, 5005, 1505, 2505, 3505, 4505, and 5505 (chains A, C, D, E, F, G, H, I, and J respectively). The relatively low number, 5, indicates that these waters have a rather high density.
RfactorNum. reflectionSelection details
Rfree0.2375 7964 Random
Rwork0.1811 --
all0.1811 79146 -
obs0.1811 79146 -
Refinement stepCycle: LAST / Resolution: 2.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12992 0 1 826 13819
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00973
X-RAY DIFFRACTIONc_angle_deg1.45957

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