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- PDB-4xs6: Salmonella typhimurium AhpC W81F mutant -

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Basic information

Entry
Database: PDB / ID: 4xs6
TitleSalmonella typhimurium AhpC W81F mutant
ComponentsAlkyl hydroperoxide reductase subunit C
KeywordsOXIDOREDUCTASE / peroxiredoxin / LU / 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: 3.35 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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)103,1679
Polymers103,0115
Non-polymers1564
Water00
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)206,33418
Polymers206,02210
Non-polymers3138
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area16370 Å2
ΔGint-96 kcal/mol
Surface area64540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.470, 169.920, 134.890
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: W81F
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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K

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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: 3.49 Å3/Da / Density % sol: 64.75 %
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: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 3.35→71.9 Å / Num. obs: 21119 / % possible obs: 100 % / Redundancy: 6.8 % / Net I/σ(I): 5.1
Reflection shellResolution: 3.35→3.53 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 0.8 / % possible all: 100

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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: 3.35→71.889 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 0.29 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2794 1902 4.75 %imported from 4ma9
Rwork0.2352 ---
obs0.2373 40067 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.35→71.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6382 0 4 0 6386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0396554
X-RAY DIFFRACTIONf_angle_d2.4518879
X-RAY DIFFRACTIONf_dihedral_angle_d15.9322355
X-RAY DIFFRACTIONf_chiral_restr0.111975
X-RAY DIFFRACTIONf_plane_restr0.0121167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.43380.39091200.34542754X-RAY DIFFRACTION100
3.4338-3.52670.32421080.32792762X-RAY DIFFRACTION100
3.5267-3.63040.33691140.31852747X-RAY DIFFRACTION100
3.6304-3.74760.35211340.30352729X-RAY DIFFRACTION100
3.7476-3.88150.28271230.29742704X-RAY DIFFRACTION100
3.8815-4.03690.34681680.28062725X-RAY DIFFRACTION100
4.0369-4.22070.33921670.25662689X-RAY DIFFRACTION100
4.2207-4.44310.28271490.22152698X-RAY DIFFRACTION100
4.4431-4.72150.2614960.20422774X-RAY DIFFRACTION100
4.7215-5.08590.23481420.19962712X-RAY DIFFRACTION100
5.0859-5.59760.20391390.20952727X-RAY DIFFRACTION100
5.5976-6.40710.33061610.20982695X-RAY DIFFRACTION100
6.4071-8.07060.22991350.19132740X-RAY DIFFRACTION100
8.0706-71.90540.21081460.16992709X-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)
12.77820.9914-0.73174.1598-1.36043.7794-0.08870.0636-0.06180.11780.50920.3092-0.0239-0.9442-0.25280.33190.0147-0.02990.56990.13270.4317-14.56169.478120.9631
23.4581.0012-0.57734.4785-0.50653.1111-0.00750.11140.45360.28420.31270.0324-0.8629-0.3022-0.20010.71870.18690.04890.34450.01570.4655-0.419732.0991125.1524
36.3454-0.86230.86041.6114-1.04093.17910.11460.45390.32830.03210.0822-0.1681-0.51560.5364-0.15130.6559-0.22970.0460.5202-0.09670.418827.762632.2435107.184
42.2914-0.60741.00192.61960.06821.7892-0.06080.44560.15080.1795-0.5074-0.4084-0.47060.39010.45850.7738-0.4287-0.0850.76570.06160.728449.626133.8664123.3949
52.1486-0.1505-0.32293.6955-1.19552.38790.2860.15960.3702-0.2428-0.4299-0.8926-0.06150.89080.22810.5703-0.11450.0231.01950.03990.957167.66416.1326122.61
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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