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- PDB-1me5: Crystal Structure of Mycobacterium Tuberculosis Alkylperoxidase A... -

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Basic information

Entry
Database: PDB / ID: 1me5
TitleCrystal Structure of Mycobacterium Tuberculosis Alkylperoxidase AhpD H132Q Mutant
ComponentsALKYLHYDROPEROXIDASE D
KeywordsOXIDOREDUCTASE / trimer / alpha helical
Function / homology
Function and homology information


lipoyl-dependent peroxiredoxin / alkyl hydroperoxide reductase activity / hydroperoxide reductase activity / Cell redox homeostasis / disulfide oxidoreductase activity / peroxiredoxin activity / cell redox homeostasis / peroxidase activity / response to oxidative stress / oxidoreductase activity ...lipoyl-dependent peroxiredoxin / alkyl hydroperoxide reductase activity / hydroperoxide reductase activity / Cell redox homeostasis / disulfide oxidoreductase activity / peroxiredoxin activity / cell redox homeostasis / peroxidase activity / response to oxidative stress / oxidoreductase activity / plasma membrane / cytosol
Similarity search - Function
Alkylhydroperoxidase AhpD / Alkylhydroperoxidase AhpD core / AhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Alkyl hydroperoxide reductase AhpD / Alkyl hydroperoxide reductase AhpD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNunn, C.M. / Djordjevic, S. / Ortiz de Montellano, P.R.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The mechanism of Mycobacterium tuberculosis alkylhydroperoxidase AhpD as defined by mutagenesis, crystallography, and kinetics.
Authors: Koshkin, A. / Nunn, C.M. / Djordjevic, S. / Ortiz de Montellano, P.R.
History
DepositionAug 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: 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: ALKYLHYDROPEROXIDASE D
B: ALKYLHYDROPEROXIDASE D
C: ALKYLHYDROPEROXIDASE D


Theoretical massNumber of molelcules
Total (without water)56,3753
Polymers56,3753
Non-polymers00
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-53 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.119, 58.652, 88.914
Angle α, β, γ (deg.)90.00, 120.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-229-

HOH

21B-240-

HOH

31B-291-

HOH

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Components

#1: Protein ALKYLHYDROPEROXIDASE D / AhpD protein


Mass: 18791.502 Da / Num. of mol.: 3 / Mutation: H132Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pacahpd / Production host: Escherichia coli (E. coli) / References: UniProt: P0A5N4, UniProt: P9WQB5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 1.99 Å3/Da / Density % sol: 38.35 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: AMMONIUM ACETATE, SODIUM CITRATE, PEG 4000, MOPS, KCL, EDTA, GLYCEROL, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 110K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2002 / Details: mirrors
RadiationMonochromator: SINGLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 17576 / Num. obs: 16445 / % possible obs: 93.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 50.165 Å2
Reflection shellResolution: 2.4→2.51 Å / % possible all: 87.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1LW1

1lw1


Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3504 1648 -random
Rwork0.2234 ---
all0.2394 16755 --
obs0.2349 16445 93.6 %-
Solvent computationSolvent model: cns bulk solvent model / Bsol: 83.4359 Å2 / ksol: 0.332286 e/Å3
Displacement parametersBiso mean: 45.13 Å2
Baniso -1Baniso -2Baniso -3
1--3.86 Å20 Å22.42 Å2
2--2.95 Å20 Å2
3---0.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3845 0 0 370 4215
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007785
X-RAY DIFFRACTIONc_angle_deg1.38725
X-RAY DIFFRACTIONc_dihedral_angle_d19.47033
X-RAY DIFFRACTIONc_improper_angle_d0.95348
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d19.5
X-RAY DIFFRACTIONx_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it3.1541.5
X-RAY DIFFRACTIONc_mcangle_it4.8452
X-RAY DIFFRACTIONc_scbond_it4.2292
X-RAY DIFFRACTIONc_scangle_it6.1442.5
LS refinement shellResolution: 2.4→2.49 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.52 143 9.4 %
Rwork0.4 1367 -
obs--86.09 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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