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Yorodumi- PDB-6xg7: 1.3 A Resolution Structure of the of the NHL Repeat Region of D. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xg7 | ||||||
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Title | 1.3 A Resolution Structure of the of the NHL Repeat Region of D. melanogaster Thin | ||||||
Components | Thin, isoform D | ||||||
Keywords | PROTEIN BINDING / PROTEIN-PROTEIN INTERACTION / BETA-PROPELLER / LIMB GIRDLE MUSCULAR DYSTROPHY TYPE 2H | ||||||
Function / homology | Function and homology information positive regulation of amino acid biosynthetic process / muscle cell development => GO:0055001 / larval locomotory behavior / myofibril assembly / muscle cell cellular homeostasis / striated muscle contraction / translation repressor activity / positive regulation of glycolytic process / Z disc / protein polyubiquitination ...positive regulation of amino acid biosynthetic process / muscle cell development => GO:0055001 / larval locomotory behavior / myofibril assembly / muscle cell cellular homeostasis / striated muscle contraction / translation repressor activity / positive regulation of glycolytic process / Z disc / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of translation / protein ubiquitination / zinc ion binding Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | ||||||
Authors | Kashipathy, M.M. / Lovell, S. / Battaile, K.P. / Bawa, S. / Geisbrecht, E.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol.Biol.Cell / Year: 2021 Title: Costameric integrin and sarcoglycan protein levels are altered in a Drosophila model for Limb-girdle muscular dystrophy type 2H. Authors: Bawa, S. / Gameros, S. / Baumann, K. / Brooks, D.S. / Kollhoff, J.A. / Zolkiewski, M. / Re Cecconi, A.D. / Panini, N. / Russo, M. / Piccirillo, R. / Johnson, D.K. / Kashipathy, M.M. / ...Authors: Bawa, S. / Gameros, S. / Baumann, K. / Brooks, D.S. / Kollhoff, J.A. / Zolkiewski, M. / Re Cecconi, A.D. / Panini, N. / Russo, M. / Piccirillo, R. / Johnson, D.K. / Kashipathy, M.M. / Battaile, K.P. / Lovell, S. / Bouyain, S.E.A. / Kawakami, J. / Geisbrecht, E.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xg7.cif.gz | 135.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xg7.ent.gz | 101.4 KB | Display | PDB format |
PDBx/mmJSON format | 6xg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/6xg7 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/6xg7 | HTTPS FTP |
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-Related structure data
Related structure data | 6d69S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33179.645 Da / Num. of mol.: 1 / Fragment: NHL Repeat Region Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: tn, Abba, abba, Dmel\CG15105, l(2)tn, CG15105, Dmel_CG15105 Plasmid: pT7HMT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B4LFP7, UniProt: B7YZK8*PLUS |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-PG4 / |
#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: 1.75 Å3/Da / Density % sol: 29.84 % / Mosaicity: 0.05 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% (w/v) PEG 3350, 100 mM Bis-Tris, 200 mM ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2019 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.3→46.55 Å / Num. obs: 58203 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.7 / Num. measured all: 376145 / Scaling rejects: 10 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6D69 Resolution: 1.3→33.11 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.05 / Phase error: 16.62 / Stereochemistry target values: ML Details: All atoms except waters were refined with anisotropic atomic displacement parameters.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.82 Å2 / Biso mean: 17.5089 Å2 / Biso min: 8.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→33.11 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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