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Yorodumi- PDB-2ycy: TURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ycy | ||||||
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Title | TURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND BOUND ANTAGONIST CYANOPINDOLOL | ||||||
Components | BETA-1 ADRENERGIC RECEPTOR | ||||||
Keywords | RECEPTOR / GPCR / TRANSDUCER / ANTAGONIST BOUND FORM / INTEGRAL MEMBRANE PROTEIN / G-PROTEIN COUPLED RECEPTOR / THERMOSTABILISING POINT MUTATIONS / SEVEN-HELIX RECEPTOR / 7TM RECEPTOR | ||||||
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: 3.15 Å | ||||||
Authors | Moukhametzianov, R. / Warne, T. / Edwards, P.C. / Serrano-Vega, M.J. / Leslie, A.G.W. / Tate, C.G. / Schertler, G.F.X. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Two Distinct Conformations of Helix 6 Observed in Antagonist-Bound Structures of a {Beta}1- Adrenergic Receptor. Authors: Moukhametzianov, R. / Warne, T. / Edwards, P.C. / Serrano-Vega, M.J. / Leslie, A.G.W. / Tate, C.G. / Schertler, G.F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ycy.cif.gz | 132.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ycy.ent.gz | 103.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ycy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ycy_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 2ycy_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 2ycy_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 2ycy_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/2ycy ftp://data.pdbj.org/pub/pdb/validation_reports/yc/2ycy | HTTPS FTP |
-Related structure data
Related structure data | 2ycwC 2ycxC 2yczC 2vt4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 35752.598 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-243,272-276,279-367 / Mutation: YES Source method: isolated from a genetically manipulated source Details: RESIDUES 3-32 AT THE N-TERMINUS AND RESIDUES 244-271 AND 277-278 OF THE THIRD INTRACELLULAR LOOP WERE DELETED FROM THE CONSTRUCT. THE CONSTRUCT WAS TRUNCATED AFTER RESIDUE 367 AND A HEXAHIS TAG ADDED. 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: Sugar | ChemComp-SOG / #4: Chemical | ChemComp-NA / | #5: 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: 3.04 Å3/Da / Density % sol: 59.47 % Description: DATA WERE COLLECTED IN WEDGES BY SCANNING THE MULTIPLE SPOTS ON THE CRYSTAL |
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Crystal grow | pH: 7.2 / Details: pH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→47.5 Å / Num. obs: 12442 / % possible obs: 83 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3.15→3.29 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 53 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VT4 Resolution: 3.15→47.51 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.843 / SU B: 30.355 / SU ML: 0.518 / Cross valid method: THROUGHOUT / ESU R Free: 0.593 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.34 Å2
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Refinement step | Cycle: LAST / Resolution: 3.15→47.51 Å
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Refine LS restraints |
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