+Open data
-Basic information
Entry | Database: PDB / ID: 7bvq | ||||||
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Title | Structure of human beta1 adrenergic receptor bound to carazolol | ||||||
Components | Endolysin,Beta-1 adrenergic receptor chimera | ||||||
Keywords | MEMBRANE PROTEIN / G protein coupled receptor / SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Xu, X. / Kaindl, J. / Clark, M. / Hubner, H. / Hirata, K. / Sunahara, R. / Gmeiner, P. / Kobilka, B.K. / Liu, X. | ||||||
Citation | Journal: Cell Res. / Year: 2021 Title: Binding pathway determines norepinephrine selectivity for the human beta 1 AR over beta 2 AR. Authors: Xu, X. / Kaindl, J. / Clark, M.J. / Hubner, H. / Hirata, K. / Sunahara, R.K. / Gmeiner, P. / Kobilka, B.K. / Liu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bvq.cif.gz | 216 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bvq.ent.gz | 154.9 KB | Display | PDB format |
PDBx/mmJSON format | 7bvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bvq_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7bvq_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7bvq_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 7bvq_validation.cif.gz | 49.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/7bvq ftp://data.pdbj.org/pub/pdb/validation_reports/bv/7bvq | HTTPS FTP |
-Related structure data
Related structure data | 7btsC 7bu6C 7bu7C 2rh1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 52235.879 Da / Num. of mol.: 2 / Mutation: C944T,C987A Source method: isolated from a genetically manipulated source Details: 1261 Cys to 1314 LEU are truncated region.,1261 Cys to 1314 LEU are truncated region. Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human) Gene: e, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D9IEF7, lysozyme #2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | |
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-Non-polymers , 8 types, 141 molecules
#3: Chemical | ChemComp-CLR / | ||||||||||||
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#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | ChemComp-NA / | #8: Chemical | #9: Chemical | ChemComp-PG4 / #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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Sequence details | THE GENEBANK ENTRY NP_000675 IS A REFERENCE SEQUENCE FOR THE RESIDUES FROM 171TH TO 462TH OF OF CHAIN A. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.12 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100 mM Sodium citrate, pH 5, 150-170 mM lithium sulfate, 38-42% PEG300, 3% 1,3-butanediol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 9, 2018 |
Radiation | Monochromator: liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 46879 / % possible obs: 99.7 % / Redundancy: 33.3 % / Biso Wilson estimate: 46.84 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.01 |
Reflection shell | Resolution: 2.5→2.6 Å / Num. unique obs: 5182 / CC1/2: 0.486 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2rh1 Resolution: 2.5→19.79 Å / SU ML: 0.3512 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 26.4209 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: 72.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.79 Å
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Refine LS restraints |
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LS refinement shell |
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