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- PDB-1n8j: Crystal Structure of AhpC with Active Site Cysteine mutated to Se... -

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Basic information

Entry
Database: PDB / ID: 1n8j
TitleCrystal Structure of AhpC with Active Site Cysteine mutated to Serine (C46S)
ComponentsAlkyl hydroperoxide reductase C22 protein
KeywordsOXIDOREDUCTASE / AhpC / peroxiredoxin / decamer / antioxidant / peroxidase / alkylhydroperoxide reductase / AhpF
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsWood, Z.A. / Poole, L.B. / Karplus, P.A.
CitationJournal: Science / Year: 2003
Title: Peroxiredoxin Evolution and the Regulation of Hydrogen Peroxide Signaling
Authors: Wood, Z.A. / Poole, L.B. / Karplus, P.A.
History
DepositionNov 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 9, 2012Group: Structure summary
Revision 1.4Oct 27, 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 1.5Aug 16, 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

Downloads & links

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Assembly

Deposited unit
A: Alkyl hydroperoxide reductase C22 protein
B: Alkyl hydroperoxide reductase C22 protein
C: Alkyl hydroperoxide reductase C22 protein
D: Alkyl hydroperoxide reductase C22 protein
E: Alkyl hydroperoxide reductase C22 protein
F: Alkyl hydroperoxide reductase C22 protein
G: Alkyl hydroperoxide reductase C22 protein
H: Alkyl hydroperoxide reductase C22 protein
I: Alkyl hydroperoxide reductase C22 protein
J: Alkyl hydroperoxide reductase C22 protein
K: Alkyl hydroperoxide reductase C22 protein
L: Alkyl hydroperoxide reductase C22 protein
M: Alkyl hydroperoxide reductase C22 protein
N: Alkyl hydroperoxide reductase C22 protein
O: Alkyl hydroperoxide reductase C22 protein
P: Alkyl hydroperoxide reductase C22 protein
Q: Alkyl hydroperoxide reductase C22 protein
R: Alkyl hydroperoxide reductase C22 protein
S: Alkyl hydroperoxide reductase C22 protein
T: Alkyl hydroperoxide reductase C22 protein


Theoretical massNumber of molelcules
Total (without water)412,50220
Polymers412,50220
Non-polymers00
Water28,6441590
1
A: Alkyl hydroperoxide reductase C22 protein
B: Alkyl hydroperoxide reductase C22 protein
C: Alkyl hydroperoxide reductase C22 protein
D: Alkyl hydroperoxide reductase C22 protein
E: Alkyl hydroperoxide reductase C22 protein
F: Alkyl hydroperoxide reductase C22 protein
G: Alkyl hydroperoxide reductase C22 protein
H: Alkyl hydroperoxide reductase C22 protein
I: Alkyl hydroperoxide reductase C22 protein
J: Alkyl hydroperoxide reductase C22 protein


Theoretical massNumber of molelcules
Total (without water)206,25110
Polymers206,25110
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28850 Å2
ΔGint-206 kcal/mol
Surface area66480 Å2
MethodPISA
2
K: Alkyl hydroperoxide reductase C22 protein
L: Alkyl hydroperoxide reductase C22 protein
M: Alkyl hydroperoxide reductase C22 protein
N: Alkyl hydroperoxide reductase C22 protein
O: Alkyl hydroperoxide reductase C22 protein
P: Alkyl hydroperoxide reductase C22 protein
Q: Alkyl hydroperoxide reductase C22 protein
R: Alkyl hydroperoxide reductase C22 protein
S: Alkyl hydroperoxide reductase C22 protein
T: Alkyl hydroperoxide reductase C22 protein


Theoretical massNumber of molelcules
Total (without water)206,25110
Polymers206,25110
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29010 Å2
ΔGint-205 kcal/mol
Surface area66590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.080, 107.330, 120.080
Angle α, β, γ (deg.)102.43, 116.22, 98.81
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a decamer made up of chains A,B,C,D,E,F,G,H,I,J or K,L,M,N,O,P,Q,R,S,T

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Components

#1: Protein
Alkyl hydroperoxide reductase C22 protein / AhpC


Mass: 20625.123 Da / Num. of mol.: 20 / Mutation: C46S
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1590 / 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: 2.67 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 4% PEG 4000, 10% isopropyl alcohol, 0.1M Na acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 %PEG40001reservoir
210 %isopropanol1reservoir
30.1 Msodium acetate1reservoirpH4.5
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 19, 2001 / Details: double crystal
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.17→19.99 Å / Num. all: 210095 / Num. obs: 210095 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.066 / Net I/σ(I): 12.1
Reflection shellResolution: 2.17→2.31 Å / % possible all: 74.8
Reflection
*PLUS
Num. obs: 204205 / % possible obs: 90.4 % / Rmerge(I) obs: 0.074 / Num. measured all: 836640
Reflection shell
*PLUS
% possible obs: 82 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KYG

1kyg
PDB Unreleased entry


Resolution: 2.17→19.99 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 9671 4.6 %RANDOM
Rwork0.188 ---
all0.1901 230631 --
obs0.1901 210095 89.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.3883 Å2 / ksol: 0.333622 e/Å3
Displacement parametersBiso mean: 47.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.82 Å2-3.04 Å20.6 Å2
2--2.01 Å2-4.81 Å2
3---1.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.17→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29120 0 0 1590 30710
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it2.821.5
X-RAY DIFFRACTIONc_mcangle_it4.222
X-RAY DIFFRACTIONc_scbond_it5.12
X-RAY DIFFRACTIONc_scangle_it7.512.5
LS refinement shellResolution: 2.17→2.31 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 1188 4 %
Rwork0.332 28164 -
obs-28164 74.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.187 / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shell
*PLUS
Lowest resolution: 2.28 Å / Rfactor Rfree: 0.36 / Rfactor Rwork: 0.335

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