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- PDB-1y25: structure of mycobacterial thiol peroxidase Tpx -

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Basic information

Entry
Database: PDB / ID: 1y25
Titlestructure of mycobacterial thiol peroxidase Tpx
ComponentsProbable thiol peroxidase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Cell redox homeostasis / Tolerance by Mtb to nitric oxide produced by macrophages / detoxification / response to nitrosative stress / disulfide oxidoreductase activity / peroxiredoxin activity / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / peptidoglycan-based cell wall ...Cell redox homeostasis / Tolerance by Mtb to nitric oxide produced by macrophages / detoxification / response to nitrosative stress / disulfide oxidoreductase activity / peroxiredoxin activity / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / peptidoglycan-based cell wall / peroxidase activity / response to oxidative stress / extracellular region / cytosol
Similarity search - Function
Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Thiol peroxidase / Thiol peroxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStehr, M. / Hoffmann, B. / Jger, T. / Singh, M. / Hecht, H.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of the inactive variant C60S of Mycobacterium tuberculosis thiol peroxidase
Authors: Stehr, M. / Hecht, H.J. / Jager, T. / Flohe, L. / Singh, M.
History
DepositionNov 20, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable thiol peroxidase
B: Probable thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9444
Polymers33,8262
Non-polymers1182
Water6,630368
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.089, 106.089, 65.334
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1211-

HOH

21B-2201-

HOH

31B-2287-

HOH

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Components

#1: Protein Probable thiol peroxidase / thiol peroxidase Rv1932 Tpx peroxiredoxin


Mass: 16912.928 Da / Num. of mol.: 2 / Mutation: C60S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1932 tpx / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3)
References: UniProt: P66952, UniProt: P9WG35*PLUS, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 14, 2004 / Details: mirrors
RadiationMonochromator: Osmics mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→92.06 Å / Num. all: 24893 / Num. obs: 24893 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 31.673 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 19.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3567 / Rsym value: 0.26 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1psq

1psq


Resolution: 2.1→30.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.913 / SU B: 10.456 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.173 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 1274 5.2 %RANDOM
Rwork0.17076 ---
all0.17461 23364 --
obs0.17461 23364 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.707 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 8 368 2754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222426
X-RAY DIFFRACTIONr_bond_other_d0.0010.022236
X-RAY DIFFRACTIONr_angle_refined_deg2.321.9753308
X-RAY DIFFRACTIONr_angle_other_deg1.01135178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2625328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8224.46894
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74915348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7741514
X-RAY DIFFRACTIONr_chiral_restr0.1210.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022798
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02472
X-RAY DIFFRACTIONr_nbd_refined0.2280.2546
X-RAY DIFFRACTIONr_nbd_other0.2030.22230
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21189
X-RAY DIFFRACTIONr_nbtor_other0.090.21370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3280.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.220
X-RAY DIFFRACTIONr_mcbond_it1.3861.52050
X-RAY DIFFRACTIONr_mcbond_other0.3061.5678
X-RAY DIFFRACTIONr_mcangle_it1.69622618
X-RAY DIFFRACTIONr_scbond_it2.8533869
X-RAY DIFFRACTIONr_scangle_it3.9754.5690
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 90 -
Rwork0.225 1686 -
obs-1686 97 %
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)
11.49110.9998-0.68282.3567-0.64071.11250.03570.0334-0.10070.11-0.087-0.192-0.06070.08060.0513-0.036-0.01820.0036-0.0560.0359-0.035932.395-28.1796.712
20.73960.1255-0.10383.8797-1.67273.47370.0081-0.0551-0.02310.87140.1590.3067-0.5678-0.2594-0.16720.13820.05280.0893-0.07570.0241-0.098633.7484.4333.05
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1651 - 165
2X-RAY DIFFRACTION2BB1 - 1651 - 165

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