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- PDB-4xra: Salmonella typhimurium AhpC T43S mutant -

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Basic information

Entry
Database: PDB / ID: 4xra
TitleSalmonella typhimurium AhpC T43S mutant
ComponentsAlkyl hydroperoxide reductase subunit C
KeywordsOXIDOREDUCTASE / peroxiredoxin / FF / PrxI / conformation
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: 1.75 Å
AuthorsPerkins, A. / Brereton, A.E. / Nelson, K. / Parsonage, D. / Poole, L. / Karplus, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM050389 United States
CitationJournal: Antioxid.Redox Signal. / Year: 2018
Title: Experimentally Dissecting the Origins of Peroxiredoxin Catalysis.
Authors: Nelson, K.J. / Perkins, A. / Van Swearingen, A.E.D. / Hartman, S. / Brereton, A.E. / Parsonage, D. / Salsbury Jr., F.R. / Karplus, P.A. / Poole, L.B.
History
DepositionJan 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_symmetry

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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)103,66818
Polymers103,1365
Non-polymers53213
Water14,232790
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)207,33636
Polymers206,27210
Non-polymers1,06526
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area36290 Å2
ΔGint-496 kcal/mol
Surface area66130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.069, 171.920, 135.290
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-204-

K

21A-325-

HOH

31E-328-

HOH

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Components

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


Mass: 20627.162 Da / Num. of mol.: 5 / Mutation: T43S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P0A251, peroxiredoxin
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / 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: 3.58 Å3/Da / Density % sol: 65.66 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 1.2 M ammonium sulfate, 24% glycerol, 0.1 M Tris pH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.75→36.7 Å / Num. obs: 148354 / % possible obs: 99.9 % / Redundancy: 13.2 % / Net I/σ(I): 11.8
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 0.6 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MA9

4ma9


Resolution: 1.75→36.277 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.17 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 14367 4.98 %
Rwork0.1706 --
obs0.172 288581 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→36.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7135 0 17 790 7942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117524
X-RAY DIFFRACTIONf_angle_d1.19710242
X-RAY DIFFRACTIONf_dihedral_angle_d13.8262731
X-RAY DIFFRACTIONf_chiral_restr0.051115
X-RAY DIFFRACTIONf_plane_restr0.0071353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.35954800.36759150X-RAY DIFFRACTION100
1.7699-1.79070.37174890.3599131X-RAY DIFFRACTION100
1.7907-1.81250.35954590.34739200X-RAY DIFFRACTION100
1.8125-1.83550.36074680.33369125X-RAY DIFFRACTION100
1.8355-1.85960.3495000.32999097X-RAY DIFFRACTION100
1.8596-1.88510.32424960.31269145X-RAY DIFFRACTION100
1.8851-1.9120.29854680.32099177X-RAY DIFFRACTION100
1.912-1.94060.37715370.33869070X-RAY DIFFRACTION100
1.9406-1.97090.29784490.28139132X-RAY DIFFRACTION100
1.9709-2.00320.26475320.25659122X-RAY DIFFRACTION100
2.0032-2.03780.26454430.23959149X-RAY DIFFRACTION100
2.0378-2.07480.24015060.23789165X-RAY DIFFRACTION100
2.0748-2.11470.22324590.21219099X-RAY DIFFRACTION100
2.1147-2.15790.23234530.20329190X-RAY DIFFRACTION100
2.1579-2.20480.23264440.19059206X-RAY DIFFRACTION100
2.2048-2.25610.26974980.23969102X-RAY DIFFRACTION100
2.2561-2.31250.2274530.18739198X-RAY DIFFRACTION100
2.3125-2.3750.19944450.16089188X-RAY DIFFRACTION100
2.375-2.44490.19355010.16649075X-RAY DIFFRACTION100
2.4449-2.52380.20525100.169093X-RAY DIFFRACTION100
2.5238-2.61390.20415120.15849165X-RAY DIFFRACTION100
2.6139-2.71860.18264620.15739122X-RAY DIFFRACTION100
2.7186-2.84220.19575210.15879099X-RAY DIFFRACTION100
2.8422-2.9920.21434860.15829128X-RAY DIFFRACTION100
2.992-3.17940.1884990.15439110X-RAY DIFFRACTION100
3.1794-3.42470.19154720.15169163X-RAY DIFFRACTION100
3.4247-3.7690.15573910.13459223X-RAY DIFFRACTION100
3.769-4.31360.14125160.12379081X-RAY DIFFRACTION100
4.3136-5.43180.1484240.12119194X-RAY DIFFRACTION100
5.4318-36.28460.17514940.1519115X-RAY DIFFRACTION100
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)
11.54620.4177-0.01981.6957-0.8662.2737-0.03510.08510.0209-0.15360.15150.2655-0.0158-0.3799-0.13310.20430.0174-0.03680.21810.00780.204-13.773210.1995120.8237
22.31670.4813-0.50452.2356-0.13851.47220.0420.04690.16990.0824-0.01180.2743-0.2263-0.2373-0.05330.26370.0758-0.01170.1988-0.03450.2217-2.868430.891126.6362
32.9162-0.18060.43211.0642-0.24331.27210.05410.66770.1462-0.2161-0.0086-0.1684-0.17910.2389-0.04440.3434-0.04610.02910.3851-0.0120.20531.183432.398107.8792
42.0993-0.12470.21222.1710.18451.3251-0.01910.22270.1405-0.11950.0068-0.2853-0.22230.14870.01860.2914-0.11950.01280.2571-0.02260.267147.121236.0817123.8248
51.6051-0.3051-0.1052.7622-1.40291.69610.00670.0968-0.0836-0.3073-0.1338-0.66340.2870.39280.13040.27840.0210.07710.4223-0.09060.462668.41533.2967124.6336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E

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