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- PDB-6kpc: Crystal structure of an agonist bound GPCR -

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Basic information

Entry
Database: PDB / ID: 6kpc
TitleCrystal structure of an agonist bound GPCR
ComponentsCannabinoid receptor 2,Endolysin,Cannabinoid receptor 2
KeywordsMEMBRANE PROTEIN / GPCR / LCP / agonist
Function / homology
Function and homology information


cannabinoid receptor activity / negative regulation of mast cell activation / negative regulation of nitric-oxide synthase activity / negative regulation of synaptic transmission, GABAergic / negative regulation of action potential / leukocyte chemotaxis / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / response to amphetamine / sensory perception of pain / cytolysis by virus of host cell ...cannabinoid receptor activity / negative regulation of mast cell activation / negative regulation of nitric-oxide synthase activity / negative regulation of synaptic transmission, GABAergic / negative regulation of action potential / leukocyte chemotaxis / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / response to amphetamine / sensory perception of pain / cytolysis by virus of host cell / negative regulation of inflammatory response / peptidoglycan catabolic process / extrinsic component of cytoplasmic side of plasma membrane / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / perikaryon / cytolysis / response to lipopolysaccharide / host cell cytoplasm / immune response / inflammatory response / G protein-coupled receptor signaling pathway / defense response to bacterium / dendrite / integral component of plasma membrane / plasma membrane
T4-type lysozyme / Endolysin T4 type / Lysozyme-like domain superfamily / GPCR, rhodopsin-like, 7TM / Cannabinoid receptor family / Glycoside hydrolase, family 24 / Cannabinoid receptor type 2 / G protein-coupled receptor, rhodopsin-like
Endolysin / Cannabinoid receptor 2
Biological speciesHomo sapiens (human)
Enterobacteria phage RB59 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLi, X.T. / Hua, T. / Wu, L.J. / Makriyannis, A. / Wu, M. / Liu, Z.J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cannabinoid receptor 2,Endolysin,Cannabinoid receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6562
Polymers56,2101
Non-polymers4461
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)33.960, 140.220, 156.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cannabinoid receptor 2,Endolysin,Cannabinoid receptor 2 / hCB2 / CX5 / Lysis protein / Lysozyme / Muramidase / hCB2 / CX5


Mass: 56209.934 Da / Num. of mol.: 1
Details: CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 ...CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion
Mutation: G78L, T127A, T153L, G210A, C54T, C97A, R242E, G304E,G78L, T127A, T153L, G210A, R242E, G304E,G78L, T127A, T153L, G210A, R242E, G304E,G78L, T127A, T153L, G210A, C54T, C97A, R242E, G304E,G78L, T127A, T153L, G210A, R242E, G304E,G78L, T127A, T153L, G210A, R242E, G304E,G78L, T127A, T153L, G210A, C54T, C97A, R242E, G304E,G78L, T127A, T153L, G210A, R242E, G304E,G78L, T127A, T153L, G210A, R242E, G304E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage RB59 (bacteriophage)
Gene: CNR2, CB2A, CB2B, e, RB59_126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P34972, UniProt: A0A097J809, lysozyme
#2: Chemical ChemComp-8D0 / (6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-octan-2-yl)-6,6-dimethyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol


Mass: 445.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H39NO3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.31 Å3/Da / Density % sol: 67.19 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM HEPES sodium pH 7.0, 25% PEG 400, 220 mM Sodium sulfate decahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→44.78 Å / Num. obs: 11476 / % possible obs: 87.6 % / Redundancy: 2.847 % / Biso Wilson estimate: 96.93 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.171 / Rrim(I) all: 0.2 / Χ2: 0.994 / Net I/σ(I): 4.26 / Num. measured all: 32673 / Scaling rejects: 21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.2-3.282.7960.6731.2223859448530.6270.78990.4
3.28-3.373.0650.5991.5325999388480.6390.69790.4
3.37-3.472.70.5561.5820258857500.7350.66484.7
3.47-3.582.7780.4212.0420758457470.8990.49588.4
3.58-3.73.1320.4192.7324658737870.8480.48290.1
3.7-3.822.8670.313.2321198297390.8870.36589.1
3.82-3.972.7220.323.3318627686840.9030.3889.1
3.97-4.132.8750.2584.1920217807030.940.390.1
4.13-4.312.9110.2514.6919277386620.9410.29389.7
4.31-4.532.5230.2084.9115396906100.9370.24988.4
4.53-4.772.8440.1945.8916986935970.9470.22786.1
4.77-5.062.8510.1995.7915856305560.9640.23188.3
5.06-5.412.8760.1955.9914816095150.950.22784.6
5.41-5.842.920.1855.8814605735000.9750.21787.3
5.84-6.42.9690.1626.2913515194550.9580.18887.7
6.4-7.162.810.1546.9111694904160.9560.18384.9
7.16-8.262.8270.1458.6810464333700.9330.16985.5
8.26-10.122.6030.1228.817943683050.9570.14682.9
10.12-14.312.7470.0899.476733062450.9880.10380.1
14.31-44.782.9780.0749.883991881340.9950.08671.3
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5zty
Resolution: 3.2→44.78 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.871 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.48
RfactorNum. reflection% reflectionSelection details
Rfree0.262 531 4.63 %RANDOM
Rwork0.23 ---
Obs0.231 11475 87.7 %-
Displacement parametersBiso max: 262.08 Å2 / Biso mean: 118.21 Å2 / Biso min: 11.04 Å2
Baniso -1Baniso -2Baniso -3
1-20.7169 Å20 Å20 Å2
2---22.8308 Å20 Å2
3---2.1138 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: final / Resolution: 3.2→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 29 0 3500
Biso mean--114.15 --
Num. residues----445
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeNumberRestraint functionWeightDev ideal
t_dihedral_angle_d1211SINUSOIDAL2
t_trig_c_planes
t_gen_planes578HARMONIC5
t_it3581HARMONIC20
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion473SEMIHARMONIC5
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact4227SEMIHARMONIC4
t_bond_d3581HARMONIC20.009
t_angle_deg4871HARMONIC21.03
t_omega_torsion1.95
t_other_torsion19.89
LS refinement shellResolution: 3.2→3.5 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2744 130 4.83 %
Rwork0.2316 2560 -
All0.2337 2690 -
Obs--88.31 %
Refinement TLS params.

Method: refined / Refinement-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.1904-1.0658-0.37887.0911-5.820810.97730.18120.01180.15150.1045-0.5129-0.2743-0.63840.84620.3318-0.4219-0.05990.0676-0.11010.304-0.313310.6139-2.8231-32.6508
24.27570.0526-1.6961.13690.59831.75620.1452-0.54180.37250.18310.07990.1184-0.15730.0554-0.225-0.1209-0.05780.04580.0746-0.1068-0.2662-5.1493-22.92519.9196
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-ID
11{ A|19 - 315 }19 - 315
22{ A|1001 - 1160 }1001 - 1160

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