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- PDB-5lyk: CRYSTAL STRUCTURE OF INTRACELLULAR B30.2 DOMAIN OF BTN3A1 BOUND T... -

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Basic information

Entry
Database: PDB / ID: 5lyk
TitleCRYSTAL STRUCTURE OF INTRACELLULAR B30.2 DOMAIN OF BTN3A1 BOUND TO CITRATE
ComponentsButyrophilin subfamily 3 member A1
KeywordsSIGNALING PROTEIN / B30.2 / butyrophilin
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / activated T cell proliferation / regulation of cytokine production / positive regulation of cytokine production / positive regulation of type II interferon production / T cell receptor signaling pathway / adaptive immune response / external side of plasma membrane / signaling receptor binding / plasma membrane
Similarity search - Function
Butyrophilin subfamily 3, PRY/SPRY domain / : / SPRY domain / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain ...Butyrophilin subfamily 3, PRY/SPRY domain / : / SPRY domain / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / Butyrophilin subfamily 3 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMohammed, F. / Baker, A.T. / Salim, M. / Willcox, B.E.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: BTN3A1 Discriminates gamma delta T Cell Phosphoantigens from Nonantigenic Small Molecules via a Conformational Sensor in Its B30.2 Domain.
Authors: Salim, M. / Knowles, T.J. / Baker, A.T. / Davey, M.S. / Jeeves, M. / Sridhar, P. / Wilkie, J. / Willcox, C.R. / Kadri, H. / Taher, T.E. / Vantourout, P. / Hayday, A. / Mehellou, Y. / Mohammed, F. / Willcox, B.E.
History
DepositionSep 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7413
Polymers21,4891
Non-polymers2512
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint6 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.500, 125.200, 39.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Butyrophilin subfamily 3 member A1


Mass: 21489.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A1, BTF5 / Plasmid: pET26 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: O00481
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 3350 and 0.2M Ammonium Citrate tribasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.7→63 Å / Num. obs: 24696 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 22.255 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 30.13
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.7-1.80.4734.060.861187
1.8-1.90.3136.880.953194.1
1.9-20.20610.410.985196.6
2-2.10.15214.550.99199.2
2.1-2.40.10923.410.9961100
2.4-2.70.07734.370.9981100
2.7-30.05847.420.9991100
3-3.50.04263.050.9991100
3.5-40.03478.4611100
4-50.0389.3411100
5-60.03287.3911100
6-100.03185.6711100
100.03179.790.998195.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7I

4n7i


Resolution: 1.7→62.62 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.374 / SU ML: 0.065 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 1194 4.8 %RANDOM
Rwork0.181 ---
obs0.1824 23457 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 44.09 Å2 / Biso mean: 15.934 Å2 / Biso min: 2.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.66 Å20 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 1.7→62.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 0 17 184 1718
Biso mean--20.79 25.41 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221573
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9592142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8975186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50323.83673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27215253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.409159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021218
X-RAY DIFFRACTIONr_nbd_refined0.20.2668
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21059
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2154
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.27
X-RAY DIFFRACTIONr_mcbond_it1.0261.5958
X-RAY DIFFRACTIONr_mcangle_it1.6421534
X-RAY DIFFRACTIONr_scbond_it2.2473707
X-RAY DIFFRACTIONr_scangle_it3.4224.5608
X-RAY DIFFRACTIONr_rigid_bond_restr1.38131665
X-RAY DIFFRACTIONr_sphericity_free4.1793184
X-RAY DIFFRACTIONr_sphericity_bonded2.01131529
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 73 -
Rwork0.243 1465 -
all-1538 -
obs--84.51 %

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