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- PDB-5id2: Asymmetry in the active site of Mycobacterium tuberculosis AhpE u... -

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Basic information

Entry
Database: PDB / ID: 5id2
TitleAsymmetry in the active site of Mycobacterium tuberculosis AhpE upon exposure to Mycothiol
Components(Putative peroxiredoxin Rv2238c) x 2
KeywordsOXIDOREDUCTASE / Thioredoxin fold
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 / cytoplasm / cytosol
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
ACETATE ION / Alkyl hydroperoxide reductase E
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsKumar, A. / Balakrishna, A.M. / Gruber, G.
Citation
Journal: Free Radic. Biol. Med. / Year: 2016
Title: Redox chemistry of Mycobacterium tuberculosis alkylhydroperoxide reductase E (AhpE): Structural and mechanistic insight into a mycoredoxin-1 independent reductive pathway of AhpE via mycothiol
Authors: Kumar, A. / Balakrishna, A.M. / Nartey, W. / Manimekalai, M.S.S. / Gruber, G.
#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
DepositionFeb 23, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative peroxiredoxin Rv2238c
B: Putative peroxiredoxin Rv2238c
C: Putative peroxiredoxin Rv2238c
D: Putative peroxiredoxin Rv2238c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2787
Polymers73,0354
Non-polymers2433
Water4,143230
1
A: Putative peroxiredoxin Rv2238c
B: Putative peroxiredoxin Rv2238c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7615
Polymers36,5172
Non-polymers2433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-13 kcal/mol
Surface area13240 Å2
MethodPISA
2
C: Putative peroxiredoxin Rv2238c
D: Putative peroxiredoxin Rv2238c


Theoretical massNumber of molelcules
Total (without water)36,5172
Polymers36,5172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-13 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.906, 146.906, 33.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALTHRTHRAA0 - 15211 - 163
21VALVALTHRTHRBB0 - 15211 - 163
12VALVALTHRTHRAA0 - 15211 - 163
22VALVALTHRTHRCC0 - 15211 - 163
13VALVALTHRTHRAA0 - 15211 - 163
23VALVALTHRTHRDD0 - 15211 - 163
14HISHISALAALABB-3 - 1538 - 164
24HISHISALAALACC-3 - 1538 - 164
15METMETTHRTHRBB-1 - 15210 - 163
25METMETTHRTHRDD-1 - 15210 - 163
16METMETTHRTHRCC-1 - 15210 - 163
26METMETTHRTHRDD-1 - 15210 - 163

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Putative peroxiredoxin Rv2238c / Thioredoxin reductase


Mass: 18266.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: Rv2238c, MtAhpE / Plasmid: pET9D / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WIE3, peroxiredoxin
#2: Protein Putative peroxiredoxin Rv2238c / Thioredoxin reductase


Mass: 18250.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: Rv2238c, MtAhpE / Plasmid: pET9D / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WIE3, peroxiredoxin
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.48 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.8M sodium malonate pH 5.0, 0.1M sodium acetate pH 4.5, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2015 / Details: mirrors
RadiationMonochromator: Double Crystal Si(111) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→30 Å / Num. obs: 27862 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 29.01 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Net I/σ(I): 14.5
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.9 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XXU

1xxu


Resolution: 2.43→29.94 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.934 / SU B: 14.877 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.225 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20454 1387 5 %RANDOM
Rwork0.18688 ---
obs0.18777 26336 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.728 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-0 Å2-0 Å2
2--0.79 Å2-0 Å2
3----1.58 Å2
Refinement stepCycle: 1 / Resolution: 2.43→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4848 0 16 230 5094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195088
X-RAY DIFFRACTIONr_bond_other_d0.0040.024862
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.9446940
X-RAY DIFFRACTIONr_angle_other_deg1.021311012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3325640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74923.889252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88815769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7761538
X-RAY DIFFRACTIONr_chiral_restr0.0630.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215967
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021267
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A92400.11
12B92400.11
21A92890.11
22C92890.11
31A93330.1
32D93330.1
41B98140.07
42C98140.07
51B91610.12
52D91610.12
61C90840.11
62D90840.11
LS refinement shellResolution: 2.432→2.495 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 112 -
Rwork0.243 1825 -
obs--97.43 %
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)
11.1018-0.686-0.16310.68440.07450.43230.0421-0.0302-0.053-0.04830.00230.0108-0.0523-0.0182-0.04440.0252-0.02980.01930.0722-0.02560.072517.447934.5531-30.3119
20.1506-0.26520.11660.7958-0.18080.28710.0412-0.01240.0388-0.0287-0.0112-0.020.0366-0.0034-0.030.0724-0.0166-0.01340.0548-0.02310.065340.900812.0732-26.5776
30.1684-0.2493-0.19830.55550.15350.39130.00620.0041-0.03110.01590.02430.0668-0.04190.0039-0.03050.0997-0.01840.00370.0296-0.01480.092733.360158.6808-12.1871
40.6586-0.2199-0.03580.6922-0.11480.38390.0128-0.00270.0472-0.0113-0.04140.0203-0.00450.04520.02850.0358-0.02380.00850.08660.00790.064158.256637.765-15.8384
50.0077-0.00390.0150.0517-0.06210.2027-0.024-0.0028-0.014-0.01860.03580.0159-0.02490.0043-0.01180.0936-0.01880.01970.0829-0.0190.113937.828235.3766-20.7075
613.0777-3.646247.187226.333567.3884426.52921.35250.22520.41020.44550.185-1.08457.54731.5681-1.53750.39970.02050.14940.1485-0.19090.366143.006814.3618-40.7631
75.003-9.186511.67222.7872-30.619441.4912-0.353-0.59530.81630.2180.0587-0.4592-0.15090.21950.29430.24460.1131-0.07840.3134-0.2240.383733.513617.4496-11.261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 153
2X-RAY DIFFRACTION2B-3 - 153
3X-RAY DIFFRACTION3C-3 - 153
4X-RAY DIFFRACTION4D-1 - 153
5X-RAY DIFFRACTION5A301 - 353
6X-RAY DIFFRACTION5B301 - 369
7X-RAY DIFFRACTION5C201 - 260
8X-RAY DIFFRACTION5D201 - 248
9X-RAY DIFFRACTION6B201
10X-RAY DIFFRACTION7B202

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