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- PDB-4qlp: Atomic structure of tuberculosis necrotizing toxin (TNT) complexe... -

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Basic information

Entry
Database: PDB / ID: 4qlp
TitleAtomic structure of tuberculosis necrotizing toxin (TNT) complexed with its immunity factor IFT
Components
  • Alanine and proline rich protein, tuberculosis necrotizing toxin (TNT)
  • immunity factor IFT
Keywordshydrolase/protein binding / DUF4237 / NAD-binding domain / b-NAD+ glycohydrolase / factor Rv3902c renamed here as immunity factor of TNT / Membrane / hydrolase-protein binding complex
Function / homology
Function and homology information


Phagocyte cell death caused by cytosolic Mtb / : / NAD+ glycohydrolase / cell wall / host cell cytosol / porin activity / pore complex / : / monoatomic ion transport / cell outer membrane ...Phagocyte cell death caused by cytosolic Mtb / : / NAD+ glycohydrolase / cell wall / host cell cytosol / porin activity / pore complex / : / monoatomic ion transport / cell outer membrane / toxin activity / cell surface / extracellular region
Similarity search - Function
Immunity protein IFT-like / Immunity protein 61 / Tuberculosis necrotizing toxin / Tuberculosis necrotizing toxin
Similarity search - Domain/homology
Outer membrane channel protein CpnT / Immunity factor for TNT
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsCingolani, G. / Lokareddy, R.K. / Sun, J. / Siroy, A. / Speer, A. / Doornbos, K.S. / Niederweis, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: The tuberculosis necrotizing toxin kills macrophages by hydrolyzing NAD.
Authors: Sun, J. / Siroy, A. / Lokareddy, R.K. / Speer, A. / Doornbos, K.S. / Cingolani, G. / Niederweis, M.
History
DepositionJun 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Structure summary
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: immunity factor IFT
B: Alanine and proline rich protein, tuberculosis necrotizing toxin (TNT)


Theoretical massNumber of molelcules
Total (without water)42,6142
Polymers42,6142
Non-polymers00
Water12,322684
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint1 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.618, 86.295, 62.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein immunity factor IFT


Mass: 19809.291 Da / Num. of mol.: 1 / Fragment: unp residues 2-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: HKBT1_4117, Rv3902c, Rv3903c, RVBD_3902c, RVBD_3903c / Production host: Escherichia coli (E. coli) / References: UniProt: O05443
#2: Protein Alanine and proline rich protein, tuberculosis necrotizing toxin (TNT)


Mass: 22805.186 Da / Num. of mol.: 1 / Fragment: unp residues 651-846
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: HKBT1_4118, Rv3902c, Rv3903c, RVBD_3902c, RVBD_3903c / Production host: Escherichia coli (E. coli) / References: UniProt: O05442
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.2 M ammonium formate, 24% (w/v) PEG 3,350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X6A10.972
SYNCHROTRONNSLS X29A21.07
Detector
TypeIDDetectorDate
ADSC QUANTUM 270r1CCDApr 9, 2014
ADSC QUANTUM 315r2CCDApr 10, 2014
RadiationMonochromator: channel-cut Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9721
21.071
ReflectionResolution: 1.1→20 Å / Num. all: 141169 / Num. obs: 141169 / % possible obs: 90.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.6 % / Rsym value: 0.057 / Net I/σ(I): 29.5
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.1-1.148.84.5285300.52155.5
1.14-1.1810.16.68116320.446175.7
1.18-1.2412.19.88146840.337195.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1696)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4O6G

4o6g


Resolution: 1.1→20.598 Å / SU ML: 0.06 / σ(F): 1.33 / Phase error: 13.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.143 1994 1.42 %RANDOM
Rwork0.1285 ---
obs0.1287 140877 90.71 %-
all-141169 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→20.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2996 0 0 684 3680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013235
X-RAY DIFFRACTIONf_angle_d1.4024407
X-RAY DIFFRACTIONf_dihedral_angle_d13.2541213
X-RAY DIFFRACTIONf_chiral_restr0.09447
X-RAY DIFFRACTIONf_plane_restr0.01593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1001-1.12760.2118820.21055709X-RAY DIFFRACTION53
1.1276-1.15810.19511030.17467129X-RAY DIFFRACTION65
1.1581-1.19220.1661290.16058976X-RAY DIFFRACTION83
1.1922-1.23070.18591490.160110352X-RAY DIFFRACTION95
1.2307-1.27470.15451480.13910380X-RAY DIFFRACTION96
1.2747-1.32570.13731490.121610467X-RAY DIFFRACTION96
1.3257-1.3860.13461530.114610556X-RAY DIFFRACTION97
1.386-1.45910.12471520.111110593X-RAY DIFFRACTION97
1.4591-1.55050.121530.107210636X-RAY DIFFRACTION98
1.5505-1.67010.11271530.106610715X-RAY DIFFRACTION98
1.6701-1.83810.11521540.112510800X-RAY DIFFRACTION98
1.8381-2.10380.1351570.112610878X-RAY DIFFRACTION99
2.1038-2.64970.12421580.12111022X-RAY DIFFRACTION100
2.6497-20.60130.16991540.147410670X-RAY DIFFRACTION93

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