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- PDB-4x1u: The structure of AhpE from Mycobacterium tuberculosis revisited -

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Basic information

Entry
Database: PDB / ID: 4x1u
TitleThe structure of AhpE from Mycobacterium tuberculosis revisited
ComponentsPutative peroxiredoxin MT2298
KeywordsOXIDOREDUCTASE / Peroxiredoxins
Function / homology
Function and homology information


mycoredoxin-dependent peroxiredoxin / Tolerance by Mtb to nitric oxide produced by macrophages / response to nitrosative stress / peroxiredoxin activity / thioredoxin peroxidase activity / cell redox homeostasis / peroxidase activity / cellular response to oxidative stress / cytosol / cytoplasm
Similarity search - Function
: / Peroxiredoxin, AhpC-type / 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 E / Alkyl hydroperoxide reductase E
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.87 Å
AuthorsPallo, A. / Messens, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G030512N Belgium
Citation
Journal: Sci Rep / Year: 2016
Title: Revisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE.
Authors: van Bergen, L.A. / Alonso, M. / Pallo, A. / Nilsson, L. / De Proft, F. / Messens, J.
#1: Journal: J. Mol. Biol. / Year: 2005
Title: Crystal Structure of AhpE from Mycobacterium tuberculosis, a 1-Cys peroxiredoxin.
Authors: Li, S. / Peterson, N.A. / Kim, M.Y. / Kim, C.Y. / Hung, L.W. / Yu, M. / Lekin, T. / Segelke, B.W. / Lott, J.S. / Baker, E.N.
History
DepositionNov 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Oct 23, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative peroxiredoxin MT2298
B: Putative peroxiredoxin MT2298
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5487
Polymers35,0882
Non-polymers4605
Water4,306239
1
A: Putative peroxiredoxin MT2298
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7283
Polymers17,5441
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative peroxiredoxin MT2298
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8204
Polymers17,5441
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.994, 147.994, 33.711
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: -4 - 151 / Label seq-ID: 3 - 158

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Putative peroxiredoxin MT2298 / Thioredoxin reductase / Alkyl hydroxiperoxide reductase E (AhpE)


Mass: 17543.770 Da / Num. of mol.: 2 / Fragment: UNP residues 1-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2298 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WIE2, UniProt: P9WIE3*PLUS, peroxiredoxin
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.8M sodium malonate pH 5.0, 0.1M sodium acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00000, 0.97937, 0.97918, 0.95370
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979371
30.979181
40.95371
ReflectionResolution: 1.87→46.8 Å / Num. obs: 28807 / % possible obs: 99.59 % / Net I/σ(I): 1.91

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
SOLVEphasing
SCALEPACKdata scaling
HKL-2000data reduction
RefinementResolution: 1.87→46.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1832 / WRfactor Rwork: 0.1514 / FOM work R set: 0.8972 / SU B: 2.406 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1133 / SU Rfree: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1832 1828 6 %RANDOM
Rwork0.1514 28807 --
obs0.1533 30761 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.25 Å2 / Biso mean: 23.303 Å2 / Biso min: 11.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å20 Å2
2---0.52 Å2-0 Å2
3---1.03 Å2
Refinement stepCycle: final / Resolution: 1.87→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 0 30 239 2731
Biso mean--44.5 33.45 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192560
X-RAY DIFFRACTIONr_bond_other_d0.0070.022408
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.9493477
X-RAY DIFFRACTIONr_angle_other_deg1.3235512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1875318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1523.548124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33615381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1991520
X-RAY DIFFRACTIONr_chiral_restr0.1240.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212945
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02635
X-RAY DIFFRACTIONr_mcbond_it2.4942.061266
X-RAY DIFFRACTIONr_mcbond_other2.4952.0571265
X-RAY DIFFRACTIONr_mcangle_it3.5043.0651580
Refine LS restraints NCS

Ens-ID: 1 / Number: 9029 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 138 -
Rwork0.249 2041 -
all-2179 -
obs--98.55 %

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