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- PDB-5epf: Crystal structure of Peroxidoxin BcpB from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 5epf
TitleCrystal structure of Peroxidoxin BcpB from Mycobacterium tuberculosis
ComponentsPeroxiredoxin
KeywordsOXIDOREDUCTASE / Mycobacterium tuberculosis / Peroxidoxin / BcpB / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / cellular response to oxidative stress / 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
: / Putative peroxiredoxin Rv1608c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Peroxidoxin BcpB from Mycobacterium tuberculosis
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionNov 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2054
Polymers17,9511
Non-polymers2543
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-19 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.620, 72.140, 40.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Peroxiredoxin


Mass: 17950.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: LH57_08785 / Plasmid: MytuD.00904.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I6X1R8, UniProt: P9WID9*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Mycrolytic MCSG1 e6: 20% PEG 3350, 200mM Potassium sulphate ; MytuD.00904.a.B1.PW37743 at 18.3 mg/ml, cryo: 20% EG, 1 step; tray: 266501e6; puck: qmk2-10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 5, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 36250 / Num. obs: 35895 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 10.55 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.062 / Χ2: 0.99 / Net I/σ(I): 25.71 / Num. measured all: 391380
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.35-1.39110.9350.5394.8428332263725770.56597.7
1.39-1.420.9490.4535.7127796258325300.47597.9
1.42-1.460.970.3427.426943249824520.35998.2
1.46-1.510.9790.289.0626216242023830.29398.5
1.51-1.560.9860.22810.8925879238023480.23998.7
1.56-1.610.9910.18213.4924726227522490.19198.9
1.61-1.670.9930.15315.7524093221321880.1698.9
1.67-1.740.9960.12319.2323267213621100.12998.8
1.74-1.820.9960.10422.5922348204220310.10999.5
1.82-1.910.9980.0827.7921550197319610.08499.4
1.91-2.010.9980.06533.7820403187118600.06899.4
2.01-2.130.9990.05538.9919266176517620.05899.8
2.13-2.280.9990.04943.7518178166816640.05199.8
2.28-2.460.9990.04446.6117107157315720.04699.9
2.46-2.70.9990.04149.7215710145214520.043100
2.7-3.020.9990.03854.2214228131313130.039100
3.02-3.490.9990.03458.1912491117411740.036100
3.49-4.270.9990.03261.04104919989970.03499.9
4.27-6.040.9990.03260.5281468028020.034100
6.040.9990.03455.5342104774700.03698.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXmodel building
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3drn

3drn


Resolution: 1.35→50 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1741 1904 5.31 %Random selection
Rwork0.1406 33982 --
obs0.1424 35886 99.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.37 Å2 / Biso mean: 15.6777 Å2 / Biso min: 5.19 Å2
Refinement stepCycle: final / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 14 260 1456
Biso mean--27.95 29.78 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081279
X-RAY DIFFRACTIONf_angle_d0.9451744
X-RAY DIFFRACTIONf_chiral_restr0.093199
X-RAY DIFFRACTIONf_plane_restr0.007228
X-RAY DIFFRACTIONf_dihedral_angle_d13.988491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.38380.17851360.14892356X-RAY DIFFRACTION98
1.3838-1.42120.15251310.13092351X-RAY DIFFRACTION98
1.4212-1.4630.15921260.11152386X-RAY DIFFRACTION98
1.463-1.51020.14871060.11262383X-RAY DIFFRACTION98
1.5102-1.56420.16641380.11542397X-RAY DIFFRACTION99
1.5642-1.62680.14991450.11342380X-RAY DIFFRACTION99
1.6268-1.70090.1551310.11712392X-RAY DIFFRACTION99
1.7009-1.79060.15961370.12342426X-RAY DIFFRACTION99
1.7906-1.90270.18171460.13942422X-RAY DIFFRACTION99
1.9027-2.04960.18681530.14082405X-RAY DIFFRACTION99
2.0496-2.25580.1571270.14092476X-RAY DIFFRACTION100
2.2558-2.58210.16221430.15032475X-RAY DIFFRACTION100
2.5821-3.25270.19621470.15352499X-RAY DIFFRACTION100
3.2527-500.18681380.15312634X-RAY DIFFRACTION100

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