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- PDB-1xvq: Crystal structure of thiol peroxidase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1xvq
TitleCrystal structure of thiol peroxidase from Mycobacterium tuberculosis
Componentsthiol peroxidase
KeywordsOXIDOREDUCTASE / thioredoxin fold / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
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
AMMONIUM ION / YTTRIUM (III) ION / Thiol peroxidase / Thiol peroxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRho, B.S. / Pedelacq, J.D. / Hung, L.W. / Holton, J.M. / Vigil, D. / Kim, S.I. / Park, M.S. / Terwilliger, T.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Functional and Structural Characterization of a Thiol Peroxidase from Mycobacterium tuberculosis.
Authors: Rho, B.S. / Hung, L.W. / Holton, J.M. / Vigil, D. / Kim, S.I. / Park, M.S. / Terwilliger, T.C. / Pedelacq, J.D.
History
DepositionOct 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Apr 3, 2024Group: 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 / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3866
Polymers18,0831
Non-polymers3035
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: thiol peroxidase
hetero molecules

A: thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,77212
Polymers36,1662
Non-polymers60610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
Buried area1970 Å2
ΔGint-36 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.555, 64.555, 196.788
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-202-

YT3

21A-301-

NH4

31A-302-

NH4

41A-495-

HOH

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Components

#1: Protein thiol peroxidase


Mass: 18083.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: tpx / Plasmid: pET28 derivative / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P66952, UniProt: P9WG35*PLUS, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Y
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: PEG 4000, Sodium acetate, Ammonium acetate, Yttrium chloride, 2-Mercaptoethanol, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2003 / Details: mirrors
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 23548 / Num. obs: 23124 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.3
Reflection shellResolution: 1.55→1.61 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rv1932 de novo Se-Met structure (not published)

Resolution: 1.75→26.89 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2853967.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1608 9.8 %RANDOM
Rwork0.203 ---
all0.205 16371 --
obs0.203 16357 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.8468 Å2 / ksol: 0.485521 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20.62 Å20 Å2
2--1.38 Å20 Å2
3----2.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.75→26.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1143 0 5 156 1304
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.081.5
X-RAY DIFFRACTIONc_mcangle_it2.92
X-RAY DIFFRACTIONc_scbond_it3.642
X-RAY DIFFRACTIONc_scangle_it4.632.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 288 10.8 %
Rwork0.224 2379 -
obs-2667 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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