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- PDB-4ma9: Wild type Salmonella Alkyl Hydroperoxide Reductase C in its subst... -

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Basic information

Entry
Database: PDB / ID: 4ma9
TitleWild type Salmonella Alkyl Hydroperoxide Reductase C in its substrate-ready conformation
ComponentsAlkyl hydroperoxide reductase subunit C
KeywordsOXIDOREDUCTASE / thioredoxin fold / peroxidase / peroxiredoxin / Prx1 AhpC / 2-Cys Prx
Function / homology
Function and homology information


NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / cellular response to stress / 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 / 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 enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsPerkins, A. / Karplus, P.A.
CitationJournal: Biochemistry / Year: 2013
Title: The sensitive balance between the fully folded and locally unfolded conformations of a model peroxiredoxin.
Authors: Perkins, A. / Nelson, K.J. / Williams, J.R. / Parsonage, D. / Poole, L.B. / Karplus, P.A.
History
DepositionAug 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkyl hydroperoxide reductase subunit C
B: Alkyl hydroperoxide reductase subunit C
C: Alkyl hydroperoxide reductase subunit C
D: Alkyl hydroperoxide reductase subunit C
E: Alkyl hydroperoxide reductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,86917
Polymers103,2065
Non-polymers66312
Water9,062503
1
A: Alkyl hydroperoxide reductase subunit C
B: Alkyl hydroperoxide reductase subunit C
C: Alkyl hydroperoxide reductase subunit C
D: Alkyl hydroperoxide reductase subunit C
E: Alkyl hydroperoxide reductase subunit C
hetero molecules

A: Alkyl hydroperoxide reductase subunit C
B: Alkyl hydroperoxide reductase subunit C
C: Alkyl hydroperoxide reductase subunit C
D: Alkyl hydroperoxide reductase subunit C
E: Alkyl hydroperoxide reductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,73834
Polymers206,41210
Non-polymers1,32624
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area31810 Å2
ΔGint-326 kcal/mol
Surface area65900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.840, 171.150, 135.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-202-

K

21E-1465-

HOH

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Components

#1: Protein
Alkyl hydroperoxide reductase subunit C / AhpC / Alkyl hydroperoxide reductase protein C22 / Peroxiredoxin / Thioredoxin peroxidase


Mass: 20641.188 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: ahpC, ahpC STM0608, STM0608 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A251, peroxiredoxin
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 503 / 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: 3.56 Å3/Da / Density % sol: 65.43 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.4 M magnesium sulfate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97741
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: liquid nitrogen cooled dual crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.82→36.758 Å / Num. all: 125942 / Num. obs: 125942 / % possible obs: 96.7 % / Redundancy: 13 % / Biso Wilson estimate: 30.68 Å2
Reflection shellHighest resolution: 1.82 Å

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.11.4refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N8J

1n8j


Resolution: 1.82→36.758 Å / Cor.coef. Fo:Fc: 0.9543 / Cor.coef. Fo:Fc free: 0.9399 / SU R Cruickshank DPI: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.099 / SU Rfree Blow DPI: 0.099 / SU Rfree Cruickshank DPI: 0.101
Details: WATERS ARE ORDERED FROM STRONGEST DENSITY TO WEAKEST DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.24 6384 5.07 %RANDOM
Rwork0.204 ---
obs-125942 95.97 %-
Displacement parametersBiso mean: 51.53 Å2
Baniso -1Baniso -2Baniso -3
1-2.984 Å20 Å20 Å2
2---3.1658 Å20 Å2
3---0.1817 Å2
Refine analyzeLuzzati coordinate error obs: 0.278 Å
Refinement stepCycle: LAST / Resolution: 1.82→36.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7102 0 32 503 7637
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114430HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0726084HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3145SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes200HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2121HARMONIC5
X-RAY DIFFRACTIONt_it14430HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.86
X-RAY DIFFRACTIONt_other_torsion15.22
X-RAY DIFFRACTIONt_chiral_improper_torsion988SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact16099SEMIHARMONIC4
LS refinement shellResolution: 1.82→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2202 398 4.79 %
Rwork0.2151 7906 -
all0.2153 8304 -
obs--95.97 %
Refinement TLS params.Method: refined / Origin x: 26.1954 Å / Origin y: 22.8634 Å / Origin z: 120.513 Å
111213212223313233
T-0.0285 Å2-0.0241 Å20.0094 Å2--0.1139 Å2-0.1003 Å2---0.1543 Å2
L0.6745 °20.0664 °20.1718 °2-0.3876 °2-0.2612 °2--0.509 °2
S-0.0171 Å °0.1325 Å °0.0335 Å °0.0046 Å °0.0477 Å °-0.0719 Å °-0.0842 Å °0.1045 Å °-0.0307 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A1 - 163
2X-RAY DIFFRACTION1{ *|* }B1 - 186
3X-RAY DIFFRACTION1{ *|* }C1 - 186
4X-RAY DIFFRACTION1{ *|* }D1 - 186
5X-RAY DIFFRACTION1{ *|* }E1 - 186
6X-RAY DIFFRACTION1{ *|* }A1 - 163
7X-RAY DIFFRACTION1{ *|* }B1 - 186
8X-RAY DIFFRACTION1{ *|* }C1 - 186
9X-RAY DIFFRACTION1{ *|* }D1 - 186
10X-RAY DIFFRACTION1{ *|* }E1 - 186
11X-RAY DIFFRACTION1{ *|* }A1 - 163
12X-RAY DIFFRACTION1{ *|* }B1 - 186
13X-RAY DIFFRACTION1{ *|* }C1 - 186
14X-RAY DIFFRACTION1{ *|* }D1 - 186
15X-RAY DIFFRACTION1{ *|* }E1 - 186

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