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- PDB-6e8k: Legionella Longbeachae LeSH (Llo2327) bound to the human interleu... -

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Basic information

Entry
Database: PDB / ID: 6e8k
TitleLegionella Longbeachae LeSH (Llo2327) bound to the human interleukin-2 receptor beta pTyr387 peptide
Components
  • LeSH (Llo2327)
  • interleukin-2 receptor beta pTyr387 peptide
KeywordsPEPTIDE BINDING PROTEIN / Src homology 2 domain
Function / homology
Function and homology information


interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-15 receptor activity / interleukin-2 binding / interleukin-2-mediated signaling pathway / interleukin-15-mediated signaling pathway / Interleukin-15 signaling / Interleukin-2 signaling / cytokine receptor activity / immunoglobulin mediated immune response ...interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-15 receptor activity / interleukin-2 binding / interleukin-2-mediated signaling pathway / interleukin-15-mediated signaling pathway / Interleukin-15 signaling / Interleukin-2 signaling / cytokine receptor activity / immunoglobulin mediated immune response / Interleukin receptor SHC signaling / coreceptor activity / positive regulation of phagocytosis / cytokine-mediated signaling pathway / RAF/MAP kinase cascade / protein-containing complex assembly / endosome / external side of plasma membrane / negative regulation of apoptotic process / cell surface / signal transduction / membrane / plasma membrane / cytosol
Similarity search - Function
Interleukin-2 receptor subunit beta, N-terminal / Interleukin-2 receptor subunit beta N-terminal domain 1 / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / SH2 domain / Src homology 2 (SH2) domain profile. ...Interleukin-2 receptor subunit beta, N-terminal / Interleukin-2 receptor subunit beta N-terminal domain 1 / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
SH2 domain-containing protein / Interleukin-2 receptor subunit beta
Similarity search - Component
Biological speciesLegionella longbeachae serogroup 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsKaneko, T. / Li, S.S.C.
CitationJournal: Nat Commun / Year: 2018
Title: Identification and characterization of a large family of superbinding bacterial SH2 domains.
Authors: Kaneko, T. / Stogios, P.J. / Ruan, X. / Voss, C. / Evdokimova, E. / Skarina, T. / Chung, A. / Liu, X. / Li, L. / Savchenko, A. / Ensminger, A.W. / Li, S.S.
History
DepositionJul 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Oct 11, 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LeSH (Llo2327)
B: interleukin-2 receptor beta pTyr387 peptide


Theoretical massNumber of molelcules
Total (without water)21,4922
Polymers21,4922
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-8 kcal/mol
Surface area10130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.450, 64.240, 67.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein LeSH (Llo2327)


Mass: 19771.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella longbeachae serogroup 1 (strain NSW150) (bacteria)
Strain: NSW150 / Gene: LLO_2327 / Production host: Escherichia coli (E. coli) / References: UniProt: D3HJY4
#2: Protein/peptide interleukin-2 receptor beta pTyr387 peptide / Interleukin-2 receptor subunit beta / IL-2RB / High affinity IL-2 receptor subunit beta / ...Interleukin-2 receptor subunit beta / IL-2RB / High affinity IL-2 receptor subunit beta / Interleukin-15 receptor subunit beta / p70-75 / p75


Mass: 1720.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P14784
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 296 K / Method: vapor diffusion / Details: PEG3000, sodium malonate

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Data collection

DiffractionMean temperature: 114 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→34.7 Å / Num. obs: 19223 / % possible obs: 91.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 25.76 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2448 / % possible all: 86.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E8H

6e8h


Resolution: 1.71→25.92 Å / SU ML: 0.2141 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7717
RfactorNum. reflection% reflection
Rfree0.2112 1757 5.02 %
Rwork0.1883 --
obs0.1894 34992 94.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.38 Å2
Refinement stepCycle: LAST / Resolution: 1.71→25.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1331 0 0 148 1479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611363
X-RAY DIFFRACTIONf_angle_d0.81181833
X-RAY DIFFRACTIONf_chiral_restr0.0586198
X-RAY DIFFRACTIONf_plane_restr0.0042228
X-RAY DIFFRACTIONf_dihedral_angle_d3.1459838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.760.38411280.32572373X-RAY DIFFRACTION86.9
1.76-1.810.31041190.26942453X-RAY DIFFRACTION91.01
1.81-1.860.26071410.26462450X-RAY DIFFRACTION91.68
1.86-1.930.24161490.22762473X-RAY DIFFRACTION91.84
1.93-2.010.23291510.20242475X-RAY DIFFRACTION93.05
2.01-2.10.22751180.18862543X-RAY DIFFRACTION94
2.1-2.210.24541130.19022559X-RAY DIFFRACTION94.79
2.21-2.350.19151100.19992612X-RAY DIFFRACTION96.29
2.35-2.530.25941720.19752621X-RAY DIFFRACTION97.79
2.53-2.790.20531680.19342616X-RAY DIFFRACTION98.93
2.79-3.190.24661310.19112701X-RAY DIFFRACTION99.96
3.19-4.010.15241610.15652678X-RAY DIFFRACTION100
4.01-25.920.1919960.17342681X-RAY DIFFRACTION98.23
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)
12.652840616780.757541069719-0.7242330696073.063724337880.2949104296812.99326465310.0505456822945-0.08723738806320.103426676110.106778460108-0.005796385701110.1114298489740.00912012407273-0.00894802644292-0.03019390849310.1279523004590.013263202232-0.01909331547880.113569818885-0.007767683901770.1265344773785.4731128147728.762973861712.6686208641
21.01762346611.70519936872-0.4506072257.19796565286-5.201980019656.78091002070.318263222025-0.762277253827-0.2593391602921.463200807380.2408066491681.07665503372-0.601063593625-0.153130163342-0.5991771987030.4466214131920.06739508718480.1326242492680.4589054951750.1041791545780.43512798719213.41512265549.6313956036815.3751757237
33.324304653810.3971387171820.1109621048368.11559451893-6.158614062237.08018355318-0.063165017086-0.128847303274-0.2354705073750.275978789021-0.149392687927-0.913042815706-0.1754485736240.1625208794620.1888948074690.1591938571830.0483530638070.02405048732310.24397706335-0.0342639258920.22289559340320.896528897915.99084510286.48600708788
40.4848189006980.1194442446560.2012646071640.8562333565060.5268775205661.126720321410.3761169871681.375155337481.17119982974-0.460615135301-0.825006633983-0.763616422681-0.9090913536921.435636868220.3634744320160.991878283469-0.04771918777830.3869498772531.251730070880.1941733766990.78745268392917.789891039140.6379064292-3.95680556369
51.854027245020.864778899894-0.7592959981996.476072708973.488012287867.469939189810.04014796683280.205573985120.265096283771-0.1878555608330.268248895178-0.166025305658-0.5169694000220.127739200531-0.2248629968380.1896802522340.0450476923991-0.01995730517840.1691317416980.03250698837880.2191715272666.4821380944436.35490621075.89874694509
63.904756904013.101694393831.571964438483.140221309311.795488960453.0465514121-0.63254485287-0.79955159461-1.603076054091.556369926310.8740543838580.01254208861781.507331235320.268284177226-0.1669561491980.5047623624790.1147894567240.1011829765750.2969836225660.04789383371250.48688789833210.885751339320.00229137714.0632146575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 130 )
5X-RAY DIFFRACTION5chain 'A' and (resid 131 through 167 )
6X-RAY DIFFRACTION6chain 'B' and (resid 386 through 388 )

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