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- PDB-4o5r: Crystal structure of Alkylhydroperoxide Reductase subunit C from ... -

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Basic information

Entry
Database: PDB / ID: 4o5r
TitleCrystal structure of Alkylhydroperoxide Reductase subunit C from E. coli
ComponentsAhpC component, subunit of alkylhydroperoxide reductase
KeywordsOXIDOREDUCTASE / hydrogen peroxide
Function / homology
Function and homology information


NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / peroxiredoxin activity / thioredoxin peroxidase activity / cellular response to stress / cell redox homeostasis / hydrogen peroxide catabolic process / peroxidase activity / response to oxidative stress / cytoplasm / 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 / Alkyl hydroperoxide reductase C
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsDip, P.V. / Kamariah, N. / Manimekalai, M.S.S. / Gruber, G. / Eisenhaber, F. / Eisenhaber, B.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF from Escherichia coli
Authors: Dip, P.V. / Kamariah, N. / Subramanian Manimekalai, M.S. / Nartey, W. / Balakrishna, A.M. / Eisenhaber, F. / Eisenhaber, B. / Gruber, G.
#1: Journal: Science / Year: 2003
Title: Peroxiredoxin Evolution and the Regulation of Hydrogen Peroxide Signaling
Authors: Wood, Z.A. / Poole, L.B. / Karplus, P.A.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Nov 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AhpC component, subunit of alkylhydroperoxide reductase
B: AhpC component, subunit of alkylhydroperoxide reductase
C: AhpC component, subunit of alkylhydroperoxide reductase
D: AhpC component, subunit of alkylhydroperoxide reductase
E: AhpC component, subunit of alkylhydroperoxide reductase


Theoretical massNumber of molelcules
Total (without water)103,9325
Polymers103,9325
Non-polymers00
Water00
1
A: AhpC component, subunit of alkylhydroperoxide reductase
B: AhpC component, subunit of alkylhydroperoxide reductase
C: AhpC component, subunit of alkylhydroperoxide reductase
D: AhpC component, subunit of alkylhydroperoxide reductase
E: AhpC component, subunit of alkylhydroperoxide reductase

A: AhpC component, subunit of alkylhydroperoxide reductase
B: AhpC component, subunit of alkylhydroperoxide reductase
C: AhpC component, subunit of alkylhydroperoxide reductase
D: AhpC component, subunit of alkylhydroperoxide reductase
E: AhpC component, subunit of alkylhydroperoxide reductase


Theoretical massNumber of molelcules
Total (without water)207,86410
Polymers207,86410
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area19220 Å2
ΔGint-157 kcal/mol
Surface area68830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.349, 137.349, 147.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: ASN / Beg label comp-ID: ASN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 5 - 160 / Label seq-ID: 5 - 160

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
Detailsdecamer generated by symmetry operation from the assymetric unit

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Components

#1: Protein
AhpC component, subunit of alkylhydroperoxide reductase / Alkyl hydroperoxide reductase / C22 subunit / Peroxiredoxin


Mass: 20786.412 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / BL21-DE3 / Gene: ahpC, B21_00563, ECBD_3047, ECD_00574 / 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
Has protein modificationY

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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: 3.86 Å3/Da / Density % sol: 68.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8M ammonium sulfate, 100mM MES, pH 6.5, 5% dioxane , 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
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: 3.33→147.45 Å / Num. obs: 23735 / % possible obs: 99.2 % / Observed criterion σ(I): -1 / Redundancy: 3.3 % / Rsym value: 0.067 / Net I/σ(I): 10.2
Reflection shellResolution: 3.33→3.51 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.484 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EMP

3emp


Resolution: 3.33→29.74 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.826 / Occupancy max: 1 / Occupancy min: 0.8 / SU B: 52.831 / SU ML: 0.354 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.519 / ESU R Free: 0.481 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1165 5.1 %RANDOM
Rwork0.241 ---
obs0.241 21621 94.9 %-
all-22790 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.65 Å20 Å2
2---0.65 Å20 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 3.33→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6555 0 0 0 6555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0196710
X-RAY DIFFRACTIONr_bond_other_d0.0010.026226
X-RAY DIFFRACTIONr_angle_refined_deg0.6961.9379092
X-RAY DIFFRACTIONr_angle_other_deg0.6253.00114363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0775827
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72524.615325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.865151109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6321530
X-RAY DIFFRACTIONr_chiral_restr0.0440.2997
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217627
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021549
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2402 / Refine-ID: X-RAY DIFFRACTION / Type: medium positional / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A0.46
2B0.45
3C0.51
4D0.58
5E0.57
LS refinement shellResolution: 3.33→3.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 82 -
Rwork0.34 1424 -
obs--86.75 %
Refinement TLS params.Method: refined / Origin x: -58.6958 Å / Origin y: -6.3236 Å / Origin z: 21.5913 Å
111213212223313233
T0.2768 Å20.0946 Å20.0671 Å2-0.0961 Å20.0349 Å2--0.0797 Å2
L0.7475 °2-0.1002 °2-0.0208 °2-0.2801 °20.2485 °2--0.3563 °2
S0.1284 Å °0.1824 Å °-0.0154 Å °-0.1122 Å °0.0112 Å °-0.0684 Å °-0.0635 Å °-0.0138 Å °-0.1396 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 167
2X-RAY DIFFRACTION1B1 - 166
3X-RAY DIFFRACTION1C1 - 167
4X-RAY DIFFRACTION1D1 - 167
5X-RAY DIFFRACTION1E1 - 165

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