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- PDB-4mab: Resolving Cys to Ala variant of Salmonella Alkyl Hydroperoxide Re... -

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Basic information

Entry
Database: PDB / ID: 4mab
TitleResolving Cys to Ala variant of Salmonella Alkyl Hydroperoxide Reductase C in its substrate-ready conformation
ComponentsAlkyl hydroperoxide reductase subunit C
KeywordsOXIDOREDUCTASE / thioredoxin fold / Prx1 / Prx / resolving Cys mutant / peroxidase / peroxiredoxin
Function / homology
Function and homology information


NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / 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 ...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: 1.9 Å
AuthorsPerkins, A. / Nelson, K.J. / Williams, J.R. / Poole, L.B. / 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 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Sep 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 / struct_conn / struct_ref_seq_dif / 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.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_ref_seq_dif.details / _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)103,56713
Polymers103,0465
Non-polymers5218
Water4,179232
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)207,13326
Polymers206,09110
Non-polymers1,04216
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area29570 Å2
ΔGint-212 kcal/mol
Surface area66980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.230, 172.420, 136.210
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-201-

K

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Components

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


Mass: 20609.123 Da / Num. of mol.: 5 / Mutation: C165A
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-K / POTASSIUM ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 3.62 Å3/Da / Density % sol: 66.07 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.4 M magnesium sulfate, 0.1 M MES, 20 uM hydrogen peroxide, 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: 1.00001
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: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.9→29.15 Å / Num. all: 117432 / Num. obs: 117418 / % possible obs: 100 % / Redundancy: 6.8 %

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Processing

Software
NameClassification
PHENIXrefinement
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MA9

4ma9


Resolution: 1.9→29.15 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.7591 / SU ML: 0.31 / σ(F): 0 / Phase error: 30.52 / Stereochemistry target values: ML
Details: WATERS ARE ORDERED FROM STRONGEST DENSITY TO WEAKEST DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.239 4791 4.99 %FROM 4MA9
Rwork0.198 91271 --
obs-96062 81.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.56 Å2 / Biso mean: 62.3451 Å2 / Biso min: 14.95 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7114 0 28 232 7374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0177360
X-RAY DIFFRACTIONf_angle_d1.7389980
X-RAY DIFFRACTIONf_chiral_restr0.0841100
X-RAY DIFFRACTIONf_plane_restr0.0111297
X-RAY DIFFRACTIONf_dihedral_angle_d14.3782643
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92180.5607120.471962085
1.9218-1.94440.493820.499881832
1.9444-1.96810.718970.383879862
1.9681-1.9930.3737160.40813093258
1.993-2.01920.4681940.37141577167143
2.0192-2.04690.3771510.35562815296676
2.0469-2.07610.38351740.39143050322483
2.0761-2.10710.3641600.36773061322183
2.1071-2.140.36191450.35733039318482
2.14-2.17510.34621640.34143235339989
2.1751-2.21260.32491760.32213581375796
2.2126-2.25280.43231970.37553491368894
2.2528-2.29610.40351660.36073472363894
2.2961-2.3430.31341820.2883689387199
2.343-2.39390.28572000.26253658385899
2.3939-2.44960.30241950.25843653384899
2.4496-2.51080.30262040.267137083912100
2.5108-2.57860.28182030.247136613864100
2.5786-2.65450.28421890.242437153904100
2.6545-2.74010.26452010.246337153916100
2.7401-2.83790.26512060.234636883894100
2.8379-2.95150.29142120.221636953907100
2.9515-3.08570.26521910.203837243915100
3.0857-3.24810.22462020.202537233925100
3.2481-3.45130.24381910.187837133904100
3.4513-3.71730.20961550.170737603915100
3.7173-4.09050.17271940.159637523946100
4.0905-4.68030.18642000.13873726392699
4.6803-5.88870.17781910.15893792398399
5.8887-29.15330.21232110.189739134124100
Refinement TLS params.Method: refined / Origin x: 26.1771 Å / Origin y: 22.9691 Å / Origin z: 121.3321 Å
111213212223313233
T0.3698 Å2-0.0276 Å20.0073 Å2-0.2698 Å2-0.131 Å2--0.2523 Å2
L1.0385 °20.071 °20.1141 °2-0.4853 °2-0.2776 °2--0.4775 °2
S-0.0017 Å °0.1386 Å °0.0889 Å °-0.0285 Å °0.044 Å °-0.1101 Å °-0.0456 Å °0.1159 Å °-0.0384 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 165
2X-RAY DIFFRACTION1allB1 - 186
3X-RAY DIFFRACTION1allC1 - 186
4X-RAY DIFFRACTION1allD1 - 186
5X-RAY DIFFRACTION1allE1 - 186
6X-RAY DIFFRACTION1allA201 - 203
7X-RAY DIFFRACTION1allB201
8X-RAY DIFFRACTION1allC201
9X-RAY DIFFRACTION1allD201 - 203
10X-RAY DIFFRACTION1allA1043 - 1230
11X-RAY DIFFRACTION1allB1001 - 1225
12X-RAY DIFFRACTION1allC1002 - 1211
13X-RAY DIFFRACTION1allD1009 - 1232
14X-RAY DIFFRACTION1allE1092 - 1217

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