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- PDB-4xrd: Salmonella typhimurium AhpC W169F mutant -

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Basic information

Entry
Database: PDB / ID: 4xrd
TitleSalmonella typhimurium AhpC W169F 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPerkins, A. / Nelson, K. / Parsonage, D. / Poole, L. / Karplus, P.A.
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 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 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.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_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)103,40114
Polymers103,0115
Non-polymers3919
Water7,026390
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)206,80328
Polymers206,02210
Non-polymers78118
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area19960 Å2
ΔGint-280 kcal/mol
Surface area64290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.870, 171.200, 135.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 20602.152 Da / Num. of mol.: 5 / Mutation: W169F
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.: 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-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.: 390 / 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: 3.55 Å3/Da / Density % sol: 65.32 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.4 M MgSO4, 0.1 M MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→24.9 Å / Num. obs: 62493 / % possible obs: 96.4 % / Redundancy: 3.7 % / Net I/σ(I): 6.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 0.5 / % possible all: 98.2

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Processing

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

4ma9


Resolution: 2.3→24.705 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 28.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 6044 4.99 %imported from 4ma9
Rwork0.192 ---
obs0.1944 121223 96.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→24.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6552 0 13 390 6955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086861
X-RAY DIFFRACTIONf_angle_d1.0649316
X-RAY DIFFRACTIONf_dihedral_angle_d14.5482455
X-RAY DIFFRACTIONf_chiral_restr0.0421023
X-RAY DIFFRACTIONf_plane_restr0.0061220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.36281890.35183889X-RAY DIFFRACTION98
2.3261-2.35350.34461980.34193934X-RAY DIFFRACTION98
2.3535-2.38220.37042210.33623881X-RAY DIFFRACTION98
2.3822-2.41230.36672220.34063908X-RAY DIFFRACTION99
2.4123-2.4440.41072000.33593908X-RAY DIFFRACTION99
2.444-2.47750.36732330.33713944X-RAY DIFFRACTION99
2.4775-2.51280.3572100.3353925X-RAY DIFFRACTION99
2.5128-2.55030.3742070.32483958X-RAY DIFFRACTION99
2.5503-2.59010.37412210.3163945X-RAY DIFFRACTION99
2.5901-2.63250.40921860.31373947X-RAY DIFFRACTION99
2.6325-2.67790.35222050.30193949X-RAY DIFFRACTION99
2.6779-2.72650.34162150.30243951X-RAY DIFFRACTION99
2.7265-2.77890.29112160.2843888X-RAY DIFFRACTION99
2.7789-2.83550.26332420.25383858X-RAY DIFFRACTION98
2.8355-2.89710.33372340.25153865X-RAY DIFFRACTION98
2.8971-2.96440.32021740.24673961X-RAY DIFFRACTION98
2.9644-3.03840.28872100.23933859X-RAY DIFFRACTION97
3.0384-3.12040.29412420.2183817X-RAY DIFFRACTION97
3.1204-3.2120.26271850.21363866X-RAY DIFFRACTION97
3.212-3.31540.23451940.19583858X-RAY DIFFRACTION96
3.3154-3.43360.26481930.1843803X-RAY DIFFRACTION96
3.4336-3.57070.24441490.16493850X-RAY DIFFRACTION96
3.5707-3.73270.23051580.15213776X-RAY DIFFRACTION95
3.7327-3.92880.18531940.14773810X-RAY DIFFRACTION94
3.9288-4.17380.18852190.13463669X-RAY DIFFRACTION94
4.1738-4.49430.16062010.11723715X-RAY DIFFRACTION93
4.4943-4.94330.14151560.10973714X-RAY DIFFRACTION92
4.9433-5.65120.14761860.13233630X-RAY DIFFRACTION91
5.6512-7.09180.18791980.14013613X-RAY DIFFRACTION90
7.0918-24.70610.16561860.14333488X-RAY DIFFRACTION88
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)
11.56720.877-0.83532.1139-1.40293.8037-0.0322-0.0217-0.0788-0.12980.28080.30610.2942-0.5868-0.23890.3589-0.0056-0.05510.36640.09420.3971-14.82389.6006121.9113
22.06421.1549-0.81472.3996-0.75822.71760.0779-0.0450.26930.20720.06570.2037-0.3458-0.2302-0.10130.31070.06710.02730.262-0.02980.301-0.725832.1712125.099
33.9766-0.58650.85111.5582-0.27961.90050.06610.43230.1673-0.09620.0543-0.267-0.2450.5263-0.11490.4324-0.10070.01470.4861-0.09130.370828.85232.1341107.504
42.5653-0.17010.33182.75940.28881.4874-0.09650.2485-0.007-0.0001-0.0572-0.3866-0.20060.20330.15040.4297-0.1448-0.06280.4874-0.03710.504849.265534.715124.3939
52.3625-0.2774-0.07773.477-1.19882.33250.11340.127-0.0043-0.3408-0.2817-0.72570.32250.58420.14660.49550.03590.06840.6819-0.03460.740168.03465.8023123.5143
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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