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Yorodumi- PDB-4ami: Turkey beta1 adrenergic receptor with stabilising mutations and b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ami | ||||||
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Title | Turkey beta1 adrenergic receptor with stabilising mutations and bound biased agonist bucindolol | ||||||
Components | BETA-1 ADRENERGIC RECEPTOR | ||||||
Keywords | MEMBRANE PROTEIN / 7TMR BETA1-ADRENOCEPTOR / STABILISING MUTATIONS / BIASED AGONIST | ||||||
Function / homology | Function and homology information beta1-adrenergic receptor activity / positive regulation of heart rate by epinephrine-norepinephrine / regulation of circadian sleep/wake cycle, sleep / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / adenylate cyclase-activating adrenergic receptor signaling pathway / early endosome / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | MELEAGRIS GALLOPAVO (turkey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Warne, T. / Edwards, P.C. / Leslie, A.G. / Tate, C.G. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Crystal Structures of a Stabilized Beta1-Adrenoceptor Bound to the Biased Agonists Bucindolol and Carvedilol Authors: Warne, T. / Edwards, P.C. / Leslie, A.G. / Tate, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ami.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ami.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ami.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ami_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4ami_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4ami_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 4ami_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/4ami ftp://data.pdbj.org/pub/pdb/validation_reports/am/4ami | HTTPS FTP |
-Related structure data
Related structure data | 4amjC 2y02S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 35940.777 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-243,272-368 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MELEAGRIS GALLOPAVO (turkey) / Cell: ERYTHROCYTE / Plasmid: PBACPAK8 / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P07700 #2: Chemical | #3: Chemical | ChemComp-2CV / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ARG 68 TO SER ENGINEERED RESIDUE IN CHAIN A, MET 90 TO VAL ...ENGINEERED | Sequence details | THE FOLLOWING MUTATIONS WERE MADE TO IMPROVE THERMOSTABILITY R68S,M90V,Y227A,A282L,F327A,F338M THE ...THE FOLLOWING MUTATIONS WERE MADE TO IMPROVE THERMOSTAB | |
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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: 3.82 Å3/Da / Density % sol: 67.8 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 9 Details: 0.1 M BICINE PH 9.0, 22% PEG 600, 4 DEGREES CELSIUS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→52.1 Å / Num. obs: 17466 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / % possible all: 86.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y02 Resolution: 3.2→44.82 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.844 / SU B: 19.89 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R Free: 0.49 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.661 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→44.82 Å
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Refine LS restraints |
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