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Yorodumi- PDB-6uhs: Open-form Crystal Structure of Chimera Bt-hRyR_12 from Bacteroide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uhs | ||||||
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Title | Open-form Crystal Structure of Chimera Bt-hRyR_12 from Bacteroides thetaiotaomicron /human | ||||||
Components | Ryanodine receptor 1 chimera | ||||||
Keywords | METAL TRANSPORT / Chimera Ryanodine Receptor / Bacteroides thetaiotaomicron VPI-5482/human / Alpha Fold / PSI-BIOLOGY / MCSG / Structural Genomics / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information junctional sarcoplasmic reticulum membrane / calcium-induced calcium release activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / I band / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to caffeine / ossification involved in bone maturation / skin development ...junctional sarcoplasmic reticulum membrane / calcium-induced calcium release activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / I band / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to caffeine / ossification involved in bone maturation / skin development / organelle membrane / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / voltage-gated calcium channel activity / skeletal muscle fiber development / muscle contraction / release of sequestered calcium ion into cytosol / Ion homeostasis / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / cytoplasmic vesicle membrane / calcium channel activity / Stimuli-sensing channels / sarcolemma / Z disc / calcium ion transport / cell cortex / protein homotetramerization / calmodulin binding / response to hypoxia / calcium ion binding / extracellular exosome / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Wu, R. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To Be Published Title: Open-form Crystal Structure of Chimera Bt-hRyR_12 from Bacteroides thetaiotaomicron /human Authors: Wu, R. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uhs.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uhs.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 6uhs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/6uhs ftp://data.pdbj.org/pub/pdb/validation_reports/uh/6uhs | HTTPS FTP |
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-Related structure data
Related structure data | 4ervS 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: 25825.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria), (gene. exp.) Homo sapiens (human) Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2247, RYR1, RYDR / Plasmid: PLASMID / Details (production host): PMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: Q8A5J2, UniProt: P21817 |
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#2: 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: 2.53 Å3/Da / Density % sol: 51.38 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris:HCl pH 5.5, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 30, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97927 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.46→50 Å / Num. obs: 9148 / % possible obs: 95.7 % / Redundancy: 4 % / Biso Wilson estimate: 34.23 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.066 / Rrim(I) all: 0.137 / Χ2: 0.79 / Net I/σ(I): 6.9 / Num. measured all: 36963 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ERV Resolution: 2.46→43.47 Å / SU ML: 0.3491 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9752 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 51.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→43.47 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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