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- PDB-4gbr: N-Terminal T4 Lysozyme Fusion Facilitates Crystallization of a G ... -

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Basic information

Entry
Database: PDB / ID: 4gbr
TitleN-Terminal T4 Lysozyme Fusion Facilitates Crystallization of a G Protein Coupled Receptor
Components
  • Beta-2 adrenergic receptor
  • Lysozyme
KeywordsMEMBRANE PROTEIN/HYDROLASE / 7 transmembrane helices / G-protein coupled receptor / signal transduction / carazolol / alkylation / membrane / MEMBRANE PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / negative regulation of smooth muscle contraction / AMPA selective glutamate receptor signaling pathway / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of autophagosome maturation / heat generation / norepinephrine binding / Adrenoceptors / positive regulation of lipophagy ...positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / negative regulation of smooth muscle contraction / AMPA selective glutamate receptor signaling pathway / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of autophagosome maturation / heat generation / norepinephrine binding / Adrenoceptors / positive regulation of lipophagy / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of multicellular organism growth / response to psychosocial stress / adrenergic receptor signaling pathway / endosome to lysosome transport / diet induced thermogenesis / positive regulation of cAMP/PKA signal transduction / adenylate cyclase binding / smooth muscle contraction / bone resorption / potassium channel regulator activity / positive regulation of bone mineralization / neuronal dense core vesicle / viral release from host cell by cytolysis / intercellular bridge / regulation of sodium ion transport / adenylate cyclase-activating adrenergic receptor signaling pathway / peptidoglycan catabolic process / brown fat cell differentiation / receptor-mediated endocytosis / response to cold / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cellular response to amyloid-beta / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / mitotic spindle / Cargo recognition for clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / Clathrin-mediated endocytosis / microtubule cytoskeleton / G alpha (s) signalling events / transcription by RNA polymerase II / host cell cytoplasm / early endosome / cell surface receptor signaling pathway / lysosome / receptor complex / positive regulation of MAPK cascade / apical plasma membrane / endosome / endosome membrane / defense response to bacterium / Ub-specific processing proteases / cilium / ciliary basal body / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / membrane / nucleus / plasma membrane
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme ...Beta 2 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme / Lysozyme-like domain superfamily / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-CAU / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.993 Å
AuthorsZou, Y. / Weis, W.I. / Kobilka, B.K.
CitationJournal: Plos One / Year: 2012
Title: N-terminal t4 lysozyme fusion facilitates crystallization of a g protein coupled receptor.
Authors: Zou, Y. / Weis, W.I. / Kobilka, B.K.
History
DepositionJul 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-2 adrenergic receptor
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7303
Polymers53,4322
Non-polymers2981
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.382, 71.376, 161.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-2 adrenergic receptor / Beta-2 adrenoreceptor / Beta-2 adrenoceptor


Mass: 35092.156 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 29-365 / Mutation: M96T, M98T, N187E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRB2, ADRB2R, B2AR / References: UniProt: P07550
#2: Protein Lysozyme / Endolysin / Lysis protein / Muramidase


Mass: 18339.934 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / References: UniProt: P00720, lysozyme
#3: Chemical ChemComp-CAU / (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol / (S)-Carazolol


Mass: 298.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 15

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 293 K / pH: 6.5
Details: PEG300 37% Bis-Tris propane 0.1M Ammonium phosphate, dibasic, 0.1M, pH 6.5, lipidic cubic phase, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D
DetectorType: MAR CCD 130 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.993→50 Å / Num. obs: 4927

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Processing

Software
NameVersionClassification
APEXdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.993→29.738 Å / SU ML: 0.55 / σ(F): 1.36 / Phase error: 34.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2821 734 14.99 %
Rwork0.2649 --
obs0.2677 4895 90.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 140.384 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--21.2141 Å20 Å20 Å2
2--59.2829 Å2-0 Å2
3----38.0128 Å2
Refinement stepCycle: LAST / Resolution: 3.993→29.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3588 0 22 0 3610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043694
X-RAY DIFFRACTIONf_angle_d0.6935015
X-RAY DIFFRACTIONf_dihedral_angle_d11.451311
X-RAY DIFFRACTIONf_chiral_restr0.047581
X-RAY DIFFRACTIONf_plane_restr0.002615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9933-4.30080.40151280.3395727X-RAY DIFFRACTION83
4.3008-4.7320.34571420.3182803X-RAY DIFFRACTION90
4.732-5.41320.31961500.2888848X-RAY DIFFRACTION93
5.4132-6.80650.32521520.3136868X-RAY DIFFRACTION94
6.8065-29.73880.21911620.2126915X-RAY DIFFRACTION94

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