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- PDB-6e8i: Legionella Longbeachae LeSH (Llo2327) bound to phosphotyrosine -

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Basic information

Entry
Database: PDB / ID: 6e8i
TitleLegionella Longbeachae LeSH (Llo2327) bound to phosphotyrosine
ComponentsLeSH (Llo2327)
KeywordsPEPTIDE BINDING PROTEIN / Src homology 2 domain
Function / homologySH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / O-PHOSPHOTYROSINE / SH2 domain-containing protein
Function and homology information
Biological speciesLegionella longbeachae serogroup 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 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 29, 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

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Assembly

Deposited unit
A: LeSH (Llo2327)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0332
Polymers19,7721
Non-polymers2611
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.810, 64.140, 67.850
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: Chemical ChemComp-PTR / O-PHOSPHOTYROSINE / PHOSPHONOTYROSINE


Type: L-peptide linking / Mass: 261.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 278 K / Method: vapor diffusion / Details: PEG3000, sodium acetate, Tris-HCl

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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 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.67→34.97 Å / Num. obs: 18762 / % possible obs: 85.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.71 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 8.5
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 4 / Num. unique obs: 2479 / % possible all: 80.6

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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: 1.68→29.99 Å / SU ML: 0.2164 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.685
RfactorNum. reflection% reflection
Rfree0.2503 1751 5.04 %
Rwork0.2168 --
obs0.2185 34765 88.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.08 Å2
Refinement stepCycle: LAST / Resolution: 1.68→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1302 0 17 233 1552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611350
X-RAY DIFFRACTIONf_angle_d0.77591816
X-RAY DIFFRACTIONf_chiral_restr0.0566196
X-RAY DIFFRACTIONf_plane_restr0.005227
X-RAY DIFFRACTIONf_dihedral_angle_d3.1355829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.31981530.29042561X-RAY DIFFRACTION88.87
1.72-1.770.25361440.23062810X-RAY DIFFRACTION96.47
1.77-1.830.22921420.2192760X-RAY DIFFRACTION96.57
1.83-1.90.28151320.24462293X-RAY DIFFRACTION96.88
1.9-1.970.5027930.40641345X-RAY DIFFRACTION49.4
1.97-2.060.29241540.21932798X-RAY DIFFRACTION96.95
2.06-2.170.2484920.22012400X-RAY DIFFRACTION82.3
2.17-2.310.3286990.30232314X-RAY DIFFRACTION79.66
2.31-2.480.23571550.22672880X-RAY DIFFRACTION99.51
2.48-2.730.25871770.22252607X-RAY DIFFRACTION91.61
2.73-3.130.23381580.20462855X-RAY DIFFRACTION99.93
3.13-3.940.18691450.17652568X-RAY DIFFRACTION89.45
3.94-29.990.21441070.16732823X-RAY DIFFRACTION96.7
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)
11.890314966340.365100757887-0.4149059587061.300897270610.02107468892241.481978194540.0192201842504-0.02952765448110.00819744721514-0.005952651426-0.02505885151070.0138798011436-0.0354986247603-0.01249323161680.02696998064970.08026255643170.00600850440328-0.007677705575440.05967177384750.001247692496520.05368603042765.5109140675928.638464623612.767411981
20.976568734488-0.1930168403110.440193607688.18891943238-5.417739273913.85311708320.0805588329001-0.106687168326-0.02848489171020.0951301831632-0.0819432855362-0.0919119354888-0.07391831025840.04598882289820.0003631546739940.135287021908-0.01365669781440.01602217260.129984532401-0.03024165714220.094015771317518.87057476514.84479371738.55862043841
35.84668083231-1.86453756110.4491979780347.200169813621.185147343922.08900092024-0.1027422881730.4355212783780.536026782971-0.475016879860.0877586970987-0.454353006753-0.5364348463140.12579010078-0.02113289443680.268499074709-0.01829826259340.00722293062790.2768438233520.02795473876440.1534470461119.0256674173735.2669661588-1.54415194176
41.323554289620.489209139208-1.039751750645.272746698431.300919215652.871399941420.08052470866260.2111925821350.16106049395-0.1875521775860.102644828447-0.105368705774-0.297559012313-0.0400355464754-0.1560817564150.1326546175270.02587323075510.002537489033050.1278578333570.03460117666760.1207668985186.9221709829237.85613610159.10416047727
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 125 )
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 141 )
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 167 )

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