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- PDB-5b8a: Crystal structure of oxidized chimeric EcAhpC1-186-YFSKHN -

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Basic information

Entry
Database: PDB / ID: 5b8a
TitleCrystal structure of oxidized chimeric EcAhpC1-186-YFSKHN
ComponentsAlkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
KeywordsOXIDOREDUCTASE / Alkylhydroperoxide reductase / AhpC / Peroxiredoxins / chimeric
Function / homology
Function and homology information


response to alkyl hydroperoxide / respiratory burst involved in inflammatory response / alkyl hydroperoxide reductase complex / peptidyl-histidine phosphorylation / hydroperoxide reductase activity / cellular response to sulfate starvation / NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / leukocyte activation / negative regulation of T cell differentiation ...response to alkyl hydroperoxide / respiratory burst involved in inflammatory response / alkyl hydroperoxide reductase complex / peptidyl-histidine phosphorylation / hydroperoxide reductase activity / cellular response to sulfate starvation / NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / leukocyte activation / negative regulation of T cell differentiation / siderophore biosynthetic process / oxidoreductase activity, acting on peroxide as acceptor / regulation of hydrogen peroxide metabolic process / thioredoxin-dependent peroxiredoxin / negative regulation of lipopolysaccharide-mediated signaling pathway / thioredoxin peroxidase activity / defense response to tumor cell / response to hydroperoxide / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species / T cell homeostasis / antioxidant activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of blood coagulation / T cell proliferation / extrinsic apoptotic signaling pathway / removal of superoxide radicals / cell redox homeostasis / thymus development / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / peroxidase activity / cellular response to oxidative stress / regulation of apoptotic process / response to oxidative stress / response to lipopolysaccharide / positive regulation of MAPK cascade / negative regulation of apoptotic process / extracellular exosome / membrane / identical protein binding / cytosol / cytoplasm
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 / Peroxiredoxin-2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKamariah, N. / Sek, M.F. / Eisenhaber, B. / Eisenhaber, F. / Gruber, G.
Citation
Journal: Sci Rep / Year: 2016
Title: Transition steps in peroxide reduction and a molecular switch for peroxide robustness of prokaryotic peroxiredoxins.
Authors: Kamariah, N. / Sek, M.F. / Eisenhaber, B. / Eisenhaber, F. / Gruber, G.
#1: Journal: Acta Cryst D / Year: 2014
Title: The ups and downs in AhpF: Structure, mechanism and ensemble formation of the Alkylhydroperoxide Reductase subunits AhpC and AhpF from Escherichia coli
Authors: Dip, P.V. / Kamariah, N. / Manimekalai, M.S.S. / Nartey, W. / Balakrishna, A.M. / Eisenhaber, F. / Eisenhaber, B. / Gruber, G.
History
DepositionJun 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
B: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
C: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
D: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
E: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
F: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
G: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
H: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
I: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
J: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,75755
Polymers214,52110
Non-polymers4,23645
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.470, 134.730, 107.530
Angle α, β, γ (deg.)90.00, 111.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 1 - 160 / Label seq-ID: 1 - 160

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.421751, 0.541318, -0.727393), (0.534886, -0.499236, -0.68166), (-0.732136, -0.676564, -0.07899)186.79482, 88.29017, 213.0426
3given(0.48849, 0.021188, -0.872312), (-0.538645, 0.793811, -0.282357), (0.686468, 0.607795, 0.399182)150.64476, 82.42406, 7.48214
4given(-0.998757, -0.049633, 0.004674), (0.039127, -0.83852, -0.543464), (0.030893, -0.542605, 0.83942)155.67094, 120.33825, 36.36713
5given(-0.430649, -0.589271, -0.683594), (-0.87047, 0.471249, 0.142152), (0.238377, 0.656265, -0.715886)215.4772, 63.11684, 179.11661
6given(0.477264, 0.829378, -0.290433), (0.834561, -0.531286, -0.145751), (-0.275185, -0.172822, -0.94573)53.32016, -1.28368, 275.55429
7given(0.448793, -0.524382, 0.723608), (0.053946, 0.824155, 0.563789), (-0.892006, -0.213989, 0.398163)-35.02823, -73.63452, 150.63855
8given(0.480028, 0.522892, 0.704385), (0.506515, -0.820783, 0.264116), (0.716251, 0.229998, -0.658851)-66.33418, -20.23339, 151.52393
9given(-0.501562, -0.820465, 0.274359), (-0.531671, 0.542506, 0.650395), (-0.682467, 0.180345, -0.708318)106.17801, -29.51657, 268.59351
10given(-0.498175, 0.007335, 0.867046), (0.021792, -0.999542, 0.020977), (0.866803, 0.029344, 0.497787)3.95516, 55.07439, -5.46041

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Components

#1: Protein
Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2 / Alkyl hydroperoxide reductase protein C22 / Peroxiredoxin / SCRP-23 / Sulfate starvation-induced ...Alkyl hydroperoxide reductase protein C22 / Peroxiredoxin / SCRP-23 / Sulfate starvation-induced protein 8 / SSI8 / Thioredoxin peroxidase / Natural killer cell-enhancing factor B / NKEF-B / PRP / Thiol-specific antioxidant protein / TSA / Thioredoxin peroxidase 1 / Thioredoxin-dependent peroxide reductase 1


Mass: 21452.109 Da / Num. of mol.: 10 / Fragment: UNP RESIDUES 1-186,UNP RESIDUES 193-198
Source method: isolated from a genetically manipulated source
Details: The fusion protein of E.coli AhpC (residues 1-186) and human Prx2 (residues 193-198)
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: ahpC, b0605, JW0598, PRDX2, NKEFB, TDPX1 / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: P0AE08, UniProt: P32119, peroxiredoxin
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M ammonium sulfate, 100 mM MES pH 6.5, 5% Dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.999999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999 Å / Relative weight: 1
ReflectionResolution: 2.7→50.01 Å / Num. obs: 69616 / % possible obs: 96.1 % / Redundancy: 2.9 % / Net I/σ(I): 7.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.9 % / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O5R

4o5r


Resolution: 2.7→50.01 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.833 / SU B: 32.309 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R: 0.75 / ESU R Free: 0.367 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28963 3356 4.8 %RANDOM
Rwork0.24415 ---
obs0.24634 66235 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.408 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å2-0 Å2-1.75 Å2
2--1.19 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13164 0 247 320 13731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01913686
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212647
X-RAY DIFFRACTIONr_angle_refined_deg0.9941.94918516
X-RAY DIFFRACTIONr_angle_other_deg0.829329184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.40351659
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44424.586652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86152235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.831560
X-RAY DIFFRACTIONr_chiral_restr0.0570.22043
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02115313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023123
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0821.6936666
X-RAY DIFFRACTIONr_mcbond_other0.0821.6936665
X-RAY DIFFRACTIONr_mcangle_it0.1542.548315
X-RAY DIFFRACTIONr_mcangle_other0.1542.548316
X-RAY DIFFRACTIONr_scbond_it0.091.7857020
X-RAY DIFFRACTIONr_scbond_other0.091.7857020
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.1142.66510202
X-RAY DIFFRACTIONr_long_range_B_refined2.63113.41114671
X-RAY DIFFRACTIONr_long_range_B_other2.63113.41114671
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2469 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.570.5
Bmedium positional0.510.5
Cmedium positional0.530.5
Dmedium positional0.650.5
Emedium positional0.580.5
Fmedium positional0.550.5
Gmedium positional0.460.5
Hmedium positional0.470.5
Imedium positional0.620.5
Jmedium positional0.580.5
Amedium thermal0.592
Bmedium thermal0.662
Cmedium thermal0.632
Dmedium thermal0.692
Emedium thermal0.572
Fmedium thermal0.632
Gmedium thermal0.472
Hmedium thermal0.982
Imedium thermal0.482
Jmedium thermal0.472
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 243 -
Rwork0.344 4911 -
obs--97.15 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4345-0.11531.49641.1764-0.39252.2602-0.05920.21710.0327-0.1165-0.03980.0536-0.14850.06120.0990.14570.03320.00820.0879-0.04360.1224103.152857.1593108.6534
23.4919-0.18230.27581.7544-0.16862.0611-0.05720.07520.08540.01720.1101-0.12290.05020.0484-0.05290.114-0.00280.03090.0158-0.01780.038494.86240.805490.1493
33.40240.652-0.27961.5192-0.98461.6457-0.02030.26990.0721-0.09580.05420.24520.0381-0.2504-0.03390.148-0.01620.02280.11240.02980.160160.599240.803888.7874
42.62990.859-0.94021.8768-0.05993.0402-0.08650.3799-0.0691-0.31670.0001-0.00490.0133-0.10230.08640.1425-0.00140.02960.07520.01580.125151.673416.004495.4174
51.1907-0.342-0.21121.82230.49062.958-0.0587-0.02180.03640.05150.04370.09010.0303-0.10680.0150.0440.00960.03730.00860.01360.072236.741417.2509125.7227
61.27-0.5413-0.01561.9413-0.83122.4563-0.0202-0.0655-0.06150.1164-0.06970.0050.02750.0750.08990.0638-0.00710.04120.0215-0.02430.0968118.527739.2899134.3734
71.40020.9096-0.57912.1355-0.95492.04950.0766-0.07040.028-0.0155-0.1009-0.113-0.07570.11240.02420.06420.00470.03070.0183-0.01930.0971107.244545.0108156.4302
81.98881.5881-0.12322.8738-0.50881.03210.0619-0.2299-0.01760.187-0.1169-0.0338-0.0418-0.0280.0550.1280.02810.03210.0452-0.00680.090388.132114.2297168.3813
92.47590.72220.5591.91960.43472.1377-0.0012-0.16820.10510.01370.0219-0.04440.0057-0.0609-0.02070.09480.02940.00530.0237-0.00750.0963.856920.291168.4199
101.16950.15080.76671.2720.61533.08440.06880.0109-0.0857-0.0902-0.06480.07180.171-0.1612-0.0040.09290.01330.0120.0190.0150.111849.07851.8795142.4152
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 168
2X-RAY DIFFRACTION2B1 - 166
3X-RAY DIFFRACTION3C1 - 163
4X-RAY DIFFRACTION4D1 - 162
5X-RAY DIFFRACTION5E1 - 164
6X-RAY DIFFRACTION6F1 - 165
7X-RAY DIFFRACTION7G1 - 171
8X-RAY DIFFRACTION8H1 - 177
9X-RAY DIFFRACTION9I1 - 162
10X-RAY DIFFRACTION10J1 - 170

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