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- PDB-5uka: Salmonella typhimurium AhpC E49Q mutant -

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Basic information

Entry
Database: PDB / ID: 5uka
TitleSalmonella typhimurium AhpC E49Q mutant
ComponentsAlkyl hydroperoxide reductase subunit C
KeywordsOXIDOREDUCTASE / peroxiredoxin / FF / PrxI / conformation
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 typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 20, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionJan 24, 2018ID: 4XS8
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 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 1.2Oct 4, 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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)103,51914
Polymers103,2015
Non-polymers3189
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-108 kcal/mol
Surface area34090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.902, 171.950, 135.766
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 20640.203 Da / Num. of mol.: 5 / Mutation: E49Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: ahpC, 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 1.4 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: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→28.1 Å / Num. obs: 225895 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 36.3 Å2 / CC1/2: 0.2 / Net I/σ(I): 13.2

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ma9

4ma9


Resolution: 1.9→27.259 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 24.4
RfactorNum. reflection% reflection
Rfree0.2095 11236 4.97 %
Rwork0.1747 --
obs0.1764 225895 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 201.57 Å2 / Biso mean: 59.2794 Å2 / Biso min: 20.79 Å2
Refinement stepCycle: final / Resolution: 1.9→27.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6442 0 9 542 6993
Biso mean--65.31 55.85 -
Num. residues----818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126760
X-RAY DIFFRACTIONf_angle_d1.2549184
X-RAY DIFFRACTIONf_chiral_restr0.0581003
X-RAY DIFFRACTIONf_plane_restr0.0081211
X-RAY DIFFRACTIONf_dihedral_angle_d14.9772432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.92160.40634000.39627025742599
1.9216-1.94430.4033850.377871917576100
1.9443-1.9680.34893690.346171377506100
1.968-1.99290.34354070.33771257532100
1.9929-2.01910.33913950.323671207515100
2.0191-2.04670.32563420.310272177559100
2.0467-2.0760.29023910.298271037494100
2.076-2.10690.28823700.283272137583100
2.1069-2.13980.29483540.274471547508100
2.1398-2.17490.31043390.2771807519100
2.1749-2.21240.27543580.256671697527100
2.2124-2.25260.29583980.265771447542100
2.2526-2.29590.29483320.248372127544100
2.2959-2.34270.24963530.217171477500100
2.3427-2.39370.23083870.205872127599100
2.3937-2.44930.24713910.196470957486100
2.4493-2.51050.24544020.19771347536100
2.5105-2.57830.23424020.181271717573100
2.5783-2.65420.2353520.183971887540100
2.6542-2.73970.22463900.18971807570100
2.7397-2.83760.22044000.180670707470100
2.8376-2.95110.21814020.172771617563100
2.9511-3.08520.22193710.173671497520100
3.0852-3.24760.22123960.175671427538100
3.2476-3.45070.19473570.156571717528100
3.4507-3.71650.18522930.142372147507100
3.7165-4.08940.16963810.132671767557100
4.0894-4.67860.14893720.11371617533100
4.6786-5.88470.14643610.12271487509100
5.8847-27.26150.16613860.146171507536100
Refinement TLS params.Method: refined / Origin x: 24.9009 Å / Origin y: 23.5453 Å / Origin z: 120.5624 Å
111213212223313233
T0.2764 Å2-0.0161 Å20.0012 Å2-0.2321 Å2-0.1263 Å2--0.2195 Å2
L0.5695 °20.1124 °20.1462 °2-0.3726 °2-0.385 °2--0.2888 °2
S-0.0031 Å °0.0866 Å °0.0421 Å °0.0262 Å °0.0288 Å °-0.0604 Å °-0.0372 Å °0.0496 Å °0.0109 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 165
2X-RAY DIFFRACTION1allA201 - 428
3X-RAY DIFFRACTION1allB1 - 164
4X-RAY DIFFRACTION1allB201 - 437
5X-RAY DIFFRACTION1allC1 - 163
6X-RAY DIFFRACTION1allC201 - 424
7X-RAY DIFFRACTION1allD1 - 164
8X-RAY DIFFRACTION1allD201 - 421
9X-RAY DIFFRACTION1allE1 - 162
10X-RAY DIFFRACTION1allE201 - 331

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