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- PDB-1lw1: Crystal Structure Of Mycobacterium Tuberculosis Alkylperoxidase A... -

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Basic information

Entry
Database: PDB / ID: 1lw1
TitleCrystal Structure Of Mycobacterium Tuberculosis Alkylperoxidase Ahpd H137F mutant
ComponentsALKYLHYDROPEROXIDASE D
KeywordsOXIDOREDUCTASE / ALKYLHYDROPEROXIDASE / TUBERCULOSIS
Function / homology
Function and homology information


lipoyl-dependent peroxiredoxin / hydroperoxide reductase activity / alkyl 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 / hydroperoxide reductase activity / alkyl 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 / AhpD-like / Carboxymuconolactone decarboxylase-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: 2.3 Å
AuthorsNunn, C.M. / Djordjevic, S. / Ortiz de Montellano, P.R.
Citation
Journal: 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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Authors: Brunger, A.T. / Adams, P.D. / Clore, G.M. / Delano, W.L. / Gros, P. / Grosse-Kunstleve, R.W. / Jiang, J.-S. / Kuszewski, J. / Nilges, M. / Pannu, N.S. / Read, R.J. / Rice, L.M. / Simonson, T. / Warren, G.L.
History
DepositionMay 30, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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: ALKYLHYDROPEROXIDASE D
B: ALKYLHYDROPEROXIDASE D
C: ALKYLHYDROPEROXIDASE D


Theoretical massNumber of molelcules
Total (without water)56,4323
Polymers56,4323
Non-polymers00
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-55 kcal/mol
Surface area18680 Å2
MethodPISA
2
A: ALKYLHYDROPEROXIDASE D
B: ALKYLHYDROPEROXIDASE D
C: ALKYLHYDROPEROXIDASE D

A: ALKYLHYDROPEROXIDASE D
B: ALKYLHYDROPEROXIDASE D
C: ALKYLHYDROPEROXIDASE D


Theoretical massNumber of molelcules
Total (without water)112,8636
Polymers112,8636
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area20580 Å2
ΔGint-119 kcal/mol
Surface area34510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.603, 62.184, 89.481
Angle α, β, γ (deg.)90.00, 121.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-262-

HOH

21B-275-

HOH

31C-272-

HOH

DetailsChains A, B and C form a protein trimer

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Components

#1: Protein ALKYLHYDROPEROXIDASE D / AhpD protein


Mass: 18810.547 Da / Num. of mol.: 3 / Mutation: h137f
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Plasmid: pACAhpD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A5N4, UniProt: P9WQB5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 1.96 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100MM SODIUM CITRATE BUFFER, PH 5.6, CONTAINING 200MM AMMONIUM ACETATE AND 26% PEG 4000. MIXED IN EQUAL VOLUME WITH AHPD (4.5 MG/ML) IN 25MM MOPS BUFFER, PH 7.2, CONTAINING 50MM KCL, 10% ...Details: 100MM SODIUM CITRATE BUFFER, PH 5.6, CONTAINING 200MM AMMONIUM ACETATE AND 26% PEG 4000. MIXED IN EQUAL VOLUME WITH AHPD (4.5 MG/ML) IN 25MM MOPS BUFFER, PH 7.2, CONTAINING 50MM KCL, 10% GLYCEROL, 0.1MM EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K
Crystal grow
*PLUS
pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14.5 mg/mlprotein1drop
225 mMMOPS1droppH7.2
350 mM1dropKCl
410 %glycerol1drop
50.1 mMEDTA1drop
65.0 mMdithiothreitol1drop
7100 mMsodium citrate1reservoirpH5.6
8200 mMammonium acetate1reservoir
926 %PEG40001reservoir

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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: 2.3→50 Å / Num. all: 18648 / Num. obs: 18396 / % possible obs: 92.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.42 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.188
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.94 / % possible all: 70.3
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 396017
Reflection shell
*PLUS
% possible obs: 70.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GU9

1gu9


Resolution: 2.3→50 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1816 -random
Rwork0.1845 ---
all0.196 18396 --
obs0.19 16580 92.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 75.3875 Å2 / ksol: 0.352637 e/Å3
Displacement parametersBiso mean: 44.14 Å2
Baniso -1Baniso -2Baniso -3
1--17.05 Å20 Å21.52 Å2
2--18.6 Å20 Å2
3----1.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3887 0 0 364 4251
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d18.83
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it2.9711.5
X-RAY DIFFRACTIONc_mcangle_it4.5882
X-RAY DIFFRACTIONc_scbond_it4.4892
X-RAY DIFFRACTIONc_scangle_it6.5392.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3572 142 9 %
Rwork0.2747 --
obs-1411 70.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.83
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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