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- PDB-5tzr: GPR40 in complex with partial agonist MK-8666 -

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Basic information

Entry
Database: PDB / ID: 5tzr
TitleGPR40 in complex with partial agonist MK-8666
ComponentsFree fatty acid receptor 1,Endolysin,Free fatty acid receptor 1
KeywordsFATTY ACID BINDING PROTEIN/HYDROLASE / FFAR1 / partial agonist / FATTY ACID BINDING PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


myosin complex / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium / calcium ion binding
Similarity search - Function
Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / 7 transmembrane receptor (rhodopsin family) / EF-hand domain / EF-hand domain pair / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-MK6 / MALONATE ION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Myosin regulatory light chain LC-2, mantle muscle / Endolysin
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsLu, J. / Byrne, N. / Patel, S. / Sharma, S. / Soisson, S.M.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40.
Authors: Lu, J. / Byrne, N. / Wang, J. / Bricogne, G. / Brown, F.K. / Chobanian, H.R. / Colletti, S.L. / Di Salvo, J. / Thomas-Fowlkes, B. / Guo, Y. / Hall, D.L. / Hadix, J. / Hastings, N.B. / ...Authors: Lu, J. / Byrne, N. / Wang, J. / Bricogne, G. / Brown, F.K. / Chobanian, H.R. / Colletti, S.L. / Di Salvo, J. / Thomas-Fowlkes, B. / Guo, Y. / Hall, D.L. / Hadix, J. / Hastings, N.B. / Hermes, J.D. / Ho, T. / Howard, A.D. / Josien, H. / Kornienko, M. / Lumb, K.J. / Miller, M.W. / Patel, S.B. / Pio, B. / Plummer, C.W. / Sherborne, B.S. / Sheth, P. / Souza, S. / Tummala, S. / Vonrhein, C. / Webb, M. / Allen, S.J. / Johnston, J.M. / Weinglass, A.B. / Sharma, S. / Soisson, S.M.
History
DepositionNov 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Free fatty acid receptor 1,Endolysin,Free fatty acid receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,07814
Polymers53,1021
Non-polymers3,97613
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-9 kcal/mol
Surface area21930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.620, 62.600, 106.150
Angle α, β, γ (deg.)90.00, 108.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Free fatty acid receptor 1,Endolysin,Free fatty acid receptor 1 / G-protein coupled receptor 40 / Lysis protein / Lysozyme / Muramidase


Mass: 53102.188 Da / Num. of mol.: 1
Mutation: L42A, F88A, G103A, Y202F, R1012G, C1054T, C1097A, I1137R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: FFAR1, GPR40 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 / References: UniProt: O14842, UniProt: P00720, lysozyme

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Non-polymers , 6 types, 75 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MK6 / (5aR,6S,6aS)-3-({2',6'-dimethyl-4'-[3-(methylsulfonyl)propoxy][1,1'-biphenyl]-3-yl}methoxy)-5,5a,6,6a-tetrahydrocyclopropa[4,5]cyclopenta[1,2-c]pyridine-6-carboxylic acid


Mass: 521.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H31NO6S
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.7
Details: 25-28%PEG 400, 0.2M sodium malonate, 0.1M Tris pH7.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 30519 / Biso Wilson estimate: 42.33 Å2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.507 / CC1/2: 0.788 / % possible all: 48.2

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
HKL-2000705data reduction
HKL-2000705data scaling
REFMAC5.8.0123phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4phu

4phu


Resolution: 2.2→28.17 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.912 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.197 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.173
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1177 3.86 %RANDOM
Rwork0.2 ---
obs0.201 30508 95.7 %-
Displacement parametersBiso mean: 54.46 Å2
Baniso -1Baniso -2Baniso -3
1--15.8286 Å20 Å2-7.5805 Å2
2---0.9712 Å20 Å2
3---16.7998 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2.2→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 192 62 3526
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013538HARMONIC2
X-RAY DIFFRACTIONt_angle_deg14776HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1202SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC8
X-RAY DIFFRACTIONt_gen_planes547HARMONIC8
X-RAY DIFFRACTIONt_it3538HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.07
X-RAY DIFFRACTIONt_other_torsion16.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion434SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4135SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.308 -3.42 %
Rwork0.212 2229 -
all0.215 2308 -
obs--74.08 %

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