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- PDB-5f8u: Ligand occupancy in crystal structure of beta1-adrenergic recepto... -

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Basic information

Entry
Database: PDB / ID: 5f8u
TitleLigand occupancy in crystal structure of beta1-adrenergic receptor previously submitted by Huang et al
ComponentsBeta-1 adrenergic receptor
KeywordsSIGNALING PROTEIN / Beta1-AR / cyanopindolol
Function / homology
Function and homology information


beta1-adrenergic receptor activity / positive regulation of heart contraction / regulation of circadian sleep/wake cycle, sleep / adenylate cyclase-activating adrenergic receptor signaling pathway / early endosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Beta 1 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) ...Beta 1 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-P32 / Beta-1 adrenergic receptor
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsLeslie, A.G.W. / Warne, A. / Tate, C.G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Crystal structure of oligomeric Beta1-adrenergic G protein-coupled receptors in ligand-free basal state.
Authors: Huang, J. / Chen, S. / Zhang, J.J. / Huang, X.Y.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Dec 26, 2018Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Beta-1 adrenergic receptor
A: Beta-1 adrenergic receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0804
Polymers71,5052
Non-polymers5752
Water00
1
B: Beta-1 adrenergic receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0402
Polymers35,7531
Non-polymers2871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-1 adrenergic receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0402
Polymers35,7531
Non-polymers2871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)229.660, 79.590, 69.040
Angle α, β, γ (deg.)90.00, 101.83, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 39 - 359 / Label seq-ID: 9 - 299

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

#1: Protein Beta-1 adrenergic receptor / Beta-1 adrenoreceptor / Beta-T


Mass: 35752.598 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-243,272-276,279-367 / Mutation: R68S,M90V,Y227A,A282L,F327A,F338MC116L, C358A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey) / Gene: ADRB1 / Plasmid: PVL1393 REMA / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P07700
#2: Chemical ChemComp-P32 / 4-{[(2S)-3-(tert-butylamino)-2-hydroxypropyl]oxy}-3H-indole-2-carbonitrile


Mass: 287.357 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.95 Å3/Da / Density % sol: 75.13 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 4GPO.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→67.57 Å / Num. obs: 17463 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 6.3
Reflection shellResolution: 3.35→3.44 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.7 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0047refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gpo

4gpo


Resolution: 3.35→67.57 Å / Cor.coef. Fo:Fc: 0.735 / Cor.coef. Fo:Fc free: 0.689 / SU B: 51.193 / SU ML: 0.79 / Cross valid method: THROUGHOUT / ESU R Free: 0.833 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.38165 677 5 %RANDOM
Rwork0.34442 ---
obs0.34617 12909 76.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.724 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.28 Å2
2--1.79 Å2-0 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 3.35→67.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 42 0 4432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.024548
X-RAY DIFFRACTIONr_bond_other_d0.0040.024506
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9616210
X-RAY DIFFRACTIONr_angle_other_deg0.9983.00210256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2965548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37222.118170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.80615742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2661530
X-RAY DIFFRACTIONr_chiral_restr0.10.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024952
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021090
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.2327.5892204
X-RAY DIFFRACTIONr_mcbond_other8.2347.5822203
X-RAY DIFFRACTIONr_mcangle_it13.4111.352748
X-RAY DIFFRACTIONr_mcangle_other13.40811.3592749
X-RAY DIFFRACTIONr_scbond_it7.5348.4152337
X-RAY DIFFRACTIONr_scbond_other7.5328.4142338
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.59512.3473457
X-RAY DIFFRACTIONr_long_range_B_refined25.20372.15720046
X-RAY DIFFRACTIONr_long_range_B_other25.20372.15520047
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17673 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.01 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 3.351→3.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.481 20 -
Rwork0.332 217 -
obs--18.08 %

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