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- PDB-1knc: Structure of AhpD from Mycobacterium tuberculosis, a novel enzyme... -

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Basic information

Entry
Database: PDB / ID: 1knc
TitleStructure of AhpD from Mycobacterium tuberculosis, a novel enzyme with thioredoxin-like activity.
ComponentsAhpD protein
KeywordsELECTRON TRANSPORT / AhpD / thioredoxin / disulfide / peroxiredoxin / lpd / redox
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 / MIR / Resolution: 2 Å
AuthorsBryk, R. / Lima, C.D. / Erdjument-Bromage, H. / Tempst, P. / Nathan, C.
CitationJournal: Science / Year: 2002
Title: Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like protein.
Authors: Bryk, R. / Lima, C.D. / Erdjument-Bromage, H. / Tempst, P. / Nathan, C.
History
DepositionDec 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: AhpD protein
B: AhpD protein
C: AhpD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,03820
Polymers56,4053
Non-polymers1,63317
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11360 Å2
ΔGint-231 kcal/mol
Surface area19180 Å2
MethodPISA
2
A: AhpD protein
B: AhpD protein
C: AhpD protein
hetero molecules

A: AhpD protein
B: AhpD protein
C: AhpD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,07540
Polymers112,8096
Non-polymers3,26634
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area24110 Å2
ΔGint-478 kcal/mol
Surface area36980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.318, 108.318, 233.582
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe AhpD trimer is composed of chains A, B, and C One trimer exists in the ASU

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Components

#1: Protein AhpD protein


Mass: 18801.520 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A5N4, UniProt: P9WQB5*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5-2.5M AmSO4, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 1.5-2.5 M / Common name: ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2001
RadiationMonochromator: sag focus / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 55072 / Num. obs: 55072 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.1 Å2 / Rsym value: 0.077 / Net I/σ(I): 18
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 2.7 / Num. unique all: 5333 / Rsym value: 0.313 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 1515540 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 98.9 % / Rmerge(I) obs: 0.313

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Processing

Software
NameVersionClassification
andSOLVEmodel building
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3209216.61 / 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
Rfree0.243 2751 5 %RANDOM
Rwork0.216 ---
all-55072 --
obs-55072 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.4947 Å2 / ksol: 0.353314 e/Å3
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.87 Å2-2.59 Å20 Å2
2---4.87 Å20 Å2
3---9.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 85 338 4311
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d17.8
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 469 5.3 %
Rwork0.304 8325 -
obs--96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.929
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72
LS refinement shell
*PLUS
Rfactor Rfree: 0.309 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.304

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