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- PDB-4ql7: Crystal structure of C-terminus truncated Alkylhydroperoxide Redu... -

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Basic information

Entry
Database: PDB / ID: 4ql7
TitleCrystal structure of C-terminus truncated Alkylhydroperoxide Reductase subunit C (AhpC1-172) from E. coli
ComponentsAlkylhydroperoxide Reductase subunit C
KeywordsOXIDOREDUCTASE / Peroxiredoxin / AhpC
Function / homology
Function and homology information


NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / peroxiredoxin activity / peroxidase activity / response to oxidative stress / 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 / Alkyl hydroperoxide reductase C
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.75 Å
AuthorsKamariah, N. / Gruber, G. / Eisenhaber, F. / Eisenhaber, B.
Citation
Journal: Biochim.Biophys.Acta / Year: 2014
Title: Key roles of the Escherichia coli AhpC C-terminus in assembly and catalysis of alkylhydroperoxide reductase, an enzyme essential for the alleviation of oxidative stress.
Authors: Dip, P.V. / Kamariah, N. / Nartey, W. / Beushausen, C. / Kostyuchenko, V.A. / Ng, T.S. / Lok, S.M. / Saw, W.G. / Eisenhaber, F. / Eisenhaber, B. / Gruber, G.
#1: Journal: To be Published
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 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

Downloads & links

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Assembly

Deposited unit
A: Alkylhydroperoxide Reductase subunit C
B: Alkylhydroperoxide Reductase subunit C
C: Alkylhydroperoxide Reductase subunit C
D: Alkylhydroperoxide Reductase subunit C
E: Alkylhydroperoxide Reductase subunit C


Theoretical massNumber of molelcules
Total (without water)96,5995
Polymers96,5995
Non-polymers00
Water0
1
A: Alkylhydroperoxide Reductase subunit C
B: Alkylhydroperoxide Reductase subunit C
C: Alkylhydroperoxide Reductase subunit C
D: Alkylhydroperoxide Reductase subunit C
E: Alkylhydroperoxide Reductase subunit C

A: Alkylhydroperoxide Reductase subunit C
B: Alkylhydroperoxide Reductase subunit C
C: Alkylhydroperoxide Reductase subunit C
D: Alkylhydroperoxide Reductase subunit C
E: Alkylhydroperoxide Reductase subunit C


Theoretical massNumber of molelcules
Total (without water)193,19710
Polymers193,19710
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area19860 Å2
ΔGint-173 kcal/mol
Surface area68810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.129, 137.129, 145.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

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

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Components

#1: Protein
Alkylhydroperoxide Reductase subunit C / Alkyl hydroperoxide reductase / C22 subunit / Peroxiredoxin


Mass: 19319.705 Da / Num. of mol.: 5 / Fragment: C-terminus truncated form, UNP resides 1-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21 DE3 / Gene: ahpc / Plasmid: pET9-d1(+)-His6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: C6EK89, UniProt: A0A140NC97*PLUS, Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor, 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: 4.08 Å3/Da / Density % sol: 69.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8M ammonium sulfate, 100mM MES, pH 6.5, 10mM cobalt chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2013 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.75→30 Å / Num. obs: 16581 / % possible obs: 99.8 % / Observed criterion σ(F): -2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.6
Reflection shellResolution: 3.75→3.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2373 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLM3.3.20data reduction
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O5R

4o5r


Resolution: 3.75→30 Å / Cor.coef. Fo:Fc: 0.814 / Cor.coef. Fo:Fc free: 0.791 / SU B: 82.851 / SU ML: 0.514 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.738 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2898 797 5 %RANDOM
Rwork0.2732 ---
obs0.274 15934 95.91 %-
all-16581 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 168.36 Å2 / Biso mean: 78.177 Å2 / Biso min: 39.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.32 Å20 Å2
2---0.32 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 3.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6563 0 0 0 6563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0196719
X-RAY DIFFRACTIONr_bond_other_d0.0010.026238
X-RAY DIFFRACTIONr_angle_refined_deg0.7471.9359103
X-RAY DIFFRACTIONr_angle_other_deg0.6463.00114383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3375827
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09324.601326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.832151113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0881530
X-RAY DIFFRACTIONr_chiral_restr0.0470.2997
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027635
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021557
Refine LS restraints NCS

Ens-ID: 1 / Number: 2469 / Refine-ID: X-RAY DIFFRACTION / Type: MEDIUM POSITIONAL / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A0.72
2B0.62
3C0.64
4D0.73
5E0.79
LS refinement shellResolution: 3.751→3.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 54 -
Rwork0.371 981 -
all-1035 -
obs--86.9 %
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)
15.47630.5961-2.15082.4328-0.5166.3653-0.83390.1723-0.6877-0.71230.2902-0.57730.79590.60690.54360.4098-0.06420.12950.2909-0.09990.526857.8367-78.758210.4368
23.37530.93230.69866.7625-2.13852.045-0.10870.502-0.3324-0.6038-0.0469-0.14780.31280.28860.15550.6335-0.39790.01010.5631-0.18530.270841.7427-74.6189-9.9181
32.4659-0.50510.26355.7367-0.92662.45540.24310.32930.3968-0.5622-0.13510.36840.0658-0.1949-0.1080.5936-0.44430.06380.525-0.0210.357940.1352-39.7761-17.1086
43.71450.26410.0484.62351.64592.48910.03150.4271-0.2636-0.8210.29910.1484-0.4378-0.6682-0.33060.7652-0.4352-0.01990.71580.21060.588516.1485-31.3986-12.784
52.74610.20950.46612.67542.11473.12350.3399-0.04860.5003-0.2453-0.22730.0869-1.119-0.5044-0.11260.9375-0.09580.27650.71870.23450.693816.9894-10.632614.8581
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 166
2X-RAY DIFFRACTION2B1 - 166
3X-RAY DIFFRACTION3C1 - 170
4X-RAY DIFFRACTION4D1 - 165
5X-RAY DIFFRACTION5E1 - 165

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