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- PDB-5x33: Leukotriene B4 receptor BLT1 in complex with BIIL260 -

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Basic information

Entry
Database: PDB / ID: 5x33
TitleLeukotriene B4 receptor BLT1 in complex with BIIL260
ComponentsLTB4 receptor,Lysozyme,LTB4 receptor
KeywordsMEMBRANE PROTEIN / helix
Function / homology
Function and homology information


leukotriene receptor activity / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / membrane => GO:0016020 / defense response to bacterium / plasma membrane
Similarity search - Function
Leukotriene B4 receptor / Leukotriene B4 type 1 receptor / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM ...Leukotriene B4 receptor / Leukotriene B4 type 1 receptor / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / 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) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-7Y9 / Endolysin / LTB4 receptor
Similarity search - Component
Biological speciesCavia porcellus (domestic guinea pig)
Enterobacteria phage RB55 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsHori, T. / Hirata, K. / Yamashita, K. / Kawano, Y. / Yamamoto, M. / Yokoyama, S.
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Na+-mimicking ligands stabilize the inactive state of leukotriene B4receptor BLT1.
Authors: Hori, T. / Okuno, T. / Hirata, K. / Yamashita, K. / Kawano, Y. / Yamamoto, M. / Hato, M. / Nakamura, M. / Shimizu, T. / Yokomizo, T. / Miyano, M. / Yokoyama, S.
History
DepositionFeb 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LTB4 receptor,Lysozyme,LTB4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2222
Polymers57,7551
Non-polymers4671
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.560, 77.620, 135.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein LTB4 receptor,Lysozyme,LTB4 receptor / Leukotriene B4 receptor


Mass: 57755.121 Da / Num. of mol.: 1 / Mutation: H83G,K88G,V212A,C1054T,C1097A,S102A
Source method: isolated from a genetically manipulated source
Details: Chimera protein of UNP residues 15-213 from Q9WTK1, UNP residues 2-161 from A0A097J792, UNP residues 214-348 from Q9WTK1.
Source: (gene. exp.) Cavia porcellus (domestic guinea pig), (gene. exp.) Enterobacteria phage RB55 (virus)
Gene: Ltb4r, e, RB55_p125 / Production host: Komagataella pastoris CBS 7435 (fungus) / References: UniProt: Q9WTK1, UniProt: A0A097J792, lysozyme
#2: Chemical ChemComp-7Y9 / 4-[[3-[[4-[2-(4-hydroxyphenyl)propan-2-yl]phenoxy]methyl]phenyl]methoxy]benzenecarboximidamide


Mass: 466.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H30N2O3

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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: 62.82 %
Crystal growTemperature: 277 K / Method: lipidic cubic phase / Details: PEG 300, Bicine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→48.5 Å / Num. obs: 8291 / % possible obs: 99.9 % / Redundancy: 34.6 % / CC1/2: 0.967 / Net I/σ(I): 6.7
Reflection shellResolution: 3.7→3.92 Å / Redundancy: 31.8 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.535 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata processing
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MBS and 4K5Y

4mbs

4k5y


Resolution: 3.7→48.539 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2958 414 5.01 %
Rwork0.2484 --
obs0.2508 8262 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→48.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 35 0 3375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053448
X-RAY DIFFRACTIONf_angle_d0.8014693
X-RAY DIFFRACTIONf_dihedral_angle_d15.0042015
X-RAY DIFFRACTIONf_chiral_restr0.042556
X-RAY DIFFRACTIONf_plane_restr0.007580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7002-4.23530.35331340.27452542X-RAY DIFFRACTION100
4.2353-5.3350.26641370.23752594X-RAY DIFFRACTION100
5.335-48.54340.28161430.24042712X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.420.6852-1.06731.4328-0.01611.4670.02950.2746-0.556-0.44650.08360.28060.0671-0.1825-0.02910.0138-0.15050.02140.84970.02771.0676101.9104183.8565283.8529
21.6149-0.1861-0.57690.3542-0.26620.528-0.0057-0.2322-0.39220.1086-0.06090.144-0.12780.44890.0804-0.0142-0.0537-0.0271.09350.05080.9258101.2925183.0013299.1973
30.6544-0.15160.02090.5786-0.42060.63530.0104-0.04770.4890.1199-0.0243-0.1988-0.0985-0.30080.01130.01630.10670.04070.76310.10781.142174.7894178.9009319.7136
42.57850.9608-0.31551.027-0.5250.3012-0.00860.39570.0206-0.1560.3848-0.05350.0685-0.5876-0.25680.2732-0.0334-0.00670.7165-0.05180.88773.0932168.6446312.5627
50.2302-0.5823-0.41631.52310.44534.34930.22720.3327-0.30910.19110.016-0.53140.12460.5083-0.0980.11320.02110.10050.88460.31211.3744112.2995174.5409291.0606
68.23430.37541.95730.01580.09010.46520.0274-0.7150.8858-0.21590.1442-1.02260.18560.5857-0.15780.48180.22840.2371.2104-0.14391.0363114.0156178.7942283.4466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 148 )
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 213 or resid 900 through 1021 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1022 through 1136 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1137 through 1203 or resid 214 through 229 )
5X-RAY DIFFRACTION5chain 'A' and (resid 230 through 287 )
6X-RAY DIFFRACTION6chain 'A' and (resid 2001 through 2001 )

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