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- PDB-4ql9: Crystal structure of C-terminus truncated Alkylhydroperoxide Redu... -

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Basic information

Entry
Database: PDB / ID: 4ql9
TitleCrystal structure of C-terminus truncated Alkylhydroperoxide Reductase subunit C (AhpC1-182) from E. coli
ComponentsAlkylhydroperoxide Reductase subunit C
KeywordsOXIDOREDUCTASE / Peroxiredoxin / AhpC
Function / homology
Function and homology information


cellular response to stress / NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / peroxiredoxin activity / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / peroxidase activity / response to oxidative stress / 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 / Alkyl hydroperoxide reductase C
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsNartey, W. / Kamariah, N. / Gruber, G.
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)101,3745
Polymers101,3745
Non-polymers00
Water00
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)202,74710
Polymers202,74710
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area18920 Å2
ΔGint-140 kcal/mol
Surface area67980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.908, 136.908, 147.807
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: 20274.730 Da / Num. of mol.: 5 / Fragment: C-terminus truncated form, UNP residues 1-182
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

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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: 3.94 Å3/Da / Density % sol: 68.82 % / Mosaicity: 0.403 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M ammonium sulfate, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 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: 3.4→30 Å / Num. all: 22425 / Num. obs: 22425 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Redundancy: 7.8 % / Rmerge(I) obs: 0.096 / Χ2: 0.794 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.4-3.5280.50922230.596100
3.52-3.6680.35322160.629100
3.66-3.8380.26522220.663100
3.83-4.0380.19222220.716100
4.03-4.2880.13122120.794100
4.28-4.617.90.0922210.86799.9
4.61-5.077.80.08122501.00399.8
5.07-5.87.80.09522360.92599.7
5.8-7.297.50.07422760.93799.7
7.29-307.10.04123470.82798.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
CrystalCleardata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O5R

4o5r


Resolution: 3.4→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.918 / SU B: 49.219 / SU ML: 0.338 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.463 / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1142 5.1 %RANDOM
Rwork0.2121 ---
obs0.2133 22401 99.55 %-
all-22401 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.58 Å2 / Biso mean: 55.202 Å2 / Biso min: 28.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0.31 Å20 Å2
2---0.63 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 3.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6535 0 0 0 6535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.026689
X-RAY DIFFRACTIONr_angle_refined_deg0.7121.9369062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.625824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83424.615325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.708151108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.7611530
X-RAY DIFFRACTIONr_chiral_restr0.0450.2994
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0215125
Refine LS restraints NCS

Ens-ID: 1 / Number: 1265 / Refine-ID: X-RAY DIFFRACTION / Type: MEDIUM POSITIONAL / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A0.44
2B0.29
3C0.3
4D0.34
5E0.38
LS refinement shellResolution: 3.4→3.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 85 -
Rwork0.273 1437 -
all-1522 -
obs--99.87 %
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)
13.4302-0.0799-1.19223.4375-0.00184.5236-0.1068-0.5084-0.2450.1148-0.03060.01210.42890.06510.13740.0984-0.0055-0.06710.1301-0.01410.215139.4276-89.2554-35.6273
26.3013-1.6095-1.69293.09820.79493.3767-0.1747-0.4446-0.31660.27730.2559-0.03960.27020.1745-0.08120.10330.0677-0.10760.308-0.04870.169643.587-73.306-14.6865
35.0204-3.1044-0.79253.47950.28642.6025-0.16-0.54610.28480.4420.1492-0.0021-0.02720.24820.01080.0805-0.02460.03050.3608-0.06350.22815.0223-55.6077-7.1496
44.0648-1.47911.52993.6018-0.90464.6554-0.0411-0.4720.25980.47330.1378-0.1962-0.5132-0.0374-0.09670.3061-0.130.11380.3852-0.14270.48619.7459-29.8351-11.7328
51.7626-0.39740.84173.0736-0.47634.4622-0.07630.30430.29230.12020.19070.2353-0.5478-0.3389-0.11450.2651-0.08270.2270.50220.07370.53861.2819-20.3244-39.4049
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 165
2X-RAY DIFFRACTION2B1 - 166
3X-RAY DIFFRACTION3C1 - 166
4X-RAY DIFFRACTION4D1 - 167
5X-RAY DIFFRACTION5E1 - 165

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