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Yorodumi- PDB-8g83: Structure of NAD+ consuming protein Acinetobacter baumannii TIR domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g83 | ||||||
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Title | Structure of NAD+ consuming protein Acinetobacter baumannii TIR domain | ||||||
Components | NAD(+) hydrolase AbTIR | ||||||
Keywords | HYDROLASE / NADASE / BACTERIAL TIR / cADPR | ||||||
Function / homology | Function and homology information NAD catabolic process / NADP+ nucleosidase activity / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / signal transduction Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii 1295743 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å | ||||||
Authors | Klontz, E.H. / Wang, Y. / Glendening, G. / Carr, J. / Tsibouris, T. / Buddula, S. / Nallar, S. / Soares, A. / Snyder, G.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: The structure of NAD + consuming protein Acinetobacter baumannii TIR domain shows unique kinetics and conformations. Authors: Klontz, E. / Obi, J.O. / Wang, Y. / Glendening, G. / Carr, J. / Tsibouris, C. / Buddula, S. / Nallar, S. / Soares, A.S. / Beckett, D. / Redzic, J.S. / Eisenmesser, E. / Palm, C. / Schmidt, K. ...Authors: Klontz, E. / Obi, J.O. / Wang, Y. / Glendening, G. / Carr, J. / Tsibouris, C. / Buddula, S. / Nallar, S. / Soares, A.S. / Beckett, D. / Redzic, J.S. / Eisenmesser, E. / Palm, C. / Schmidt, K. / Scudder, A.H. / Obiorah, T. / Essuman, K. / Milbrandt, J. / Diantonio, A. / Ray, K. / Snyder, M.L.D. / Deredge, D. / Snyder, G.A. #1: Journal: J.Synchrotron Radiat. / Year: 2022 Title: AMX - the highly automated macromolecular crystallography (17-ID-1) beamline at the NSLS-II. Authors: Schneider, D.K. / Soares, A.S. / Lazo, E.O. / Kreitler, D.F. / Qian, K. / Fuchs, M.R. / Bhogadi, D.K. / Antonelli, S. / Myers, S.S. / Martins, B.S. / Skinner, J.M. / Aishima, J. / Bernstein, ...Authors: Schneider, D.K. / Soares, A.S. / Lazo, E.O. / Kreitler, D.F. / Qian, K. / Fuchs, M.R. / Bhogadi, D.K. / Antonelli, S. / Myers, S.S. / Martins, B.S. / Skinner, J.M. / Aishima, J. / Bernstein, H.J. / Langdon, T. / Lara, J. / Petkus, R. / Cowan, M. / Flaks, L. / Smith, T. / Shea-McCarthy, G. / Idir, M. / Huang, L. / Chubar, O. / Sweet, R.M. / Berman, L.E. / McSweeney, S. / Jakoncic, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g83.cif.gz | 128.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g83.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 8g83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/8g83 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/8g83 | HTTPS FTP |
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-Related structure data
Related structure data | 4lqcS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.29452954917, -0.679219895402, -0.672244507866), (-0.705478956513, -0.319976992651, 0.63238767073), (-0.644633063519, 0.660511209492, -0.384932663661)Vector: 8. ...NCS oper: (Code: given Matrix: (-0.29452954917, -0.679219895402, -0.672244507866), Vector: |
-Components
#1: Protein | Mass: 20417.607 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii 1295743 (bacteria) Gene: J512_3302 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A009IHW8, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion Details: MIDAS 2-19: 20% v/v Jeffamine M-2070, 2% v/v dimethylsulfoxide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920072 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.920072 Å / Relative weight: 1 |
Reflection | Resolution: 3.03→28.86 Å / Num. obs: 6668 / % possible obs: 98.01 % / Redundancy: 2 % / Biso Wilson estimate: 63.28 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05218 / Rpim(I) all: 0.05218 / Rrim(I) all: 0.0738 / Net I/σ(I): 10.06 |
Reflection shell | Resolution: 3.031→3.139 Å / Rmerge(I) obs: 0.308 / Num. unique obs: 639 / CC1/2: 0.793 / CC star: 0.94 / Rpim(I) all: 0.308 / Rrim(I) all: 0.435 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4LQC Resolution: 3.03→28.86 Å / SU ML: 0.4253 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3279 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.44 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.03→28.86 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.874862877213 Å | ||||||||||||||||||||||||
LS refinement shell |
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