+Open data
-Basic information
Entry | Database: PDB / ID: 8r15 | ||||||
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Title | Crystal structure of Fusarium oxysporum NADase I | ||||||
Components | TNT domain-containing protein | ||||||
Keywords | HYDROLASE / NADase / NAD hydrolase / homodimer / glycoprotein / extracellular / TNT domain / covalent dimer | ||||||
Function / homology | Tuberculosis necrotizing toxin / Tuberculosis necrotizing toxin / TNT domain-containing protein Function and homology information | ||||||
Biological species | Fusarium oxysporum f. sp. cubense race 1 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Kallio, J.P. / Ferrario, E. / Stromland, O. / Ziegler, M. | ||||||
Funding support | Norway, 1items
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Citation | Journal: Protein Sci. / Year: 2024 Title: Evolution of fungal tuberculosis necrotizing toxin (TNT) domain-containing enzymes reveals divergent adaptations to enhance NAD cleavage. Authors: Ferrario, E. / Kallio, J.P. / Emdadi, M. / Stromland, O. / Rack, J.G.M. / Ziegler, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8r15.cif.gz | 115 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8r15.ent.gz | 72.8 KB | Display | PDB format |
PDBx/mmJSON format | 8r15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8r15_validation.pdf.gz | 769.8 KB | Display | wwPDB validaton report |
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Full document | 8r15_full_validation.pdf.gz | 771 KB | Display | |
Data in XML | 8r15_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 8r15_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/8r15 ftp://data.pdbj.org/pub/pdb/validation_reports/r1/8r15 | HTTPS FTP |
-Related structure data
Related structure data | 8r17C C: citing same article (ref.) |
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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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24824.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MLPSFLLSSLLCLSTVSA = signal sequence DVLFQGPGHHHHHH= 3c protease site and His-tag Source: (gene. exp.) Fusarium oxysporum f. sp. cubense race 1 (fungus) Gene: FOC1_g10001035 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: N4U1S7 |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.88 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion / Details: polyethylene glycol (PEG) 1500, MIB buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 12, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.13 Å / Num. obs: 8352 / % possible obs: 90 % / Redundancy: 6.8 % / Biso Wilson estimate: 43.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.05 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible obs: 59.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 561 / CC1/2: 0.563 / Rpim(I) all: 0.403 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.13 Å / SU ML: 0.2671 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6482 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: 47.09 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→45.13 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.471 Å / Origin y: -28.326 Å / Origin z: 7.682 Å
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Refinement TLS group | Selection details: ( CHAIN A AND RESID 29:228 ) |