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- PDB-6e8h: Legionella Longbeachae LeSH (Llo2327) -

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Basic information

Entry
Database: PDB / ID: 6e8h
TitleLegionella Longbeachae LeSH (Llo2327)
ComponentsLeSH (Llo2327)
KeywordsPEPTIDE BINDING PROTEIN / Src homology 2 domain
Function / homologySH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / SH2 domain-containing protein
Function and homology information
Biological speciesLegionella longbeachae serogroup 1
MethodX-RAY DIFFRACTION / SAD / 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 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: LeSH (Llo2327)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8072
Polymers19,7721
Non-polymers351
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.260, 66.510, 68.210
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 278 K / Method: vapor diffusion / Details: Tris, PEG3000, sodium acetate

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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: Dec 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.66→19.63 Å / Num. obs: 22693 / % possible obs: 97.5 % / Redundancy: 55.7 % / Biso Wilson estimate: 21.17 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 68.2
Reflection shellResolution: 1.66→1.76 Å / Redundancy: 50.5 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 16.9 / Num. unique obs: 2832 / % possible all: 85

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 1.68→19.63 Å / SU ML: 0.1958 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0777
RfactorNum. reflection% reflection
Rfree0.2475 2157 5.11 %
Rwork0.2119 --
obs0.2137 42244 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.79 Å2
Refinement stepCycle: LAST / Resolution: 1.68→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 1 243 1554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591341
X-RAY DIFFRACTIONf_angle_d0.80051803
X-RAY DIFFRACTIONf_chiral_restr0.0592196
X-RAY DIFFRACTIONf_plane_restr0.0055227
X-RAY DIFFRACTIONf_dihedral_angle_d2.61827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.710.27841350.26182549X-RAY DIFFRACTION95.24
1.71-1.760.28241460.24922718X-RAY DIFFRACTION100
1.76-1.80.23571580.24622676X-RAY DIFFRACTION100
1.8-1.860.30321390.23572689X-RAY DIFFRACTION99.96
1.86-1.920.26671620.23832702X-RAY DIFFRACTION99.9
1.92-1.990.28641570.23752640X-RAY DIFFRACTION99.64
1.99-2.070.22871590.2122729X-RAY DIFFRACTION99.83
2.07-2.160.26191420.21292656X-RAY DIFFRACTION99.5
2.16-2.270.25931140.20542722X-RAY DIFFRACTION99.23
2.27-2.420.28931130.222671X-RAY DIFFRACTION98.34
2.42-2.60.27381700.232652X-RAY DIFFRACTION98.88
2.6-2.860.26531690.22432647X-RAY DIFFRACTION98.98
2.86-3.280.27741460.21052682X-RAY DIFFRACTION99.44
3.28-4.120.17721490.19352667X-RAY DIFFRACTION99.44
4.12-19.630.2535980.19012687X-RAY DIFFRACTION97.69
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)
12.764079073380.787829058648-0.07202385654744.11766332284-2.355647670045.018988566370.329008321499-0.2687370533430.0815722886626-0.0951466737278-0.305731518490.02797351168130.1890476410570.2032280897770.02974793450710.267569793646-0.02541786632980.01590889282710.159464505543-0.02323176834910.10393558215526.464909398636.845262594417.7774383612
22.90278191141.84694350994-2.251486110322.02844382171-1.045651194613.993062738-0.0476676240012-0.0750348976111-0.158275747872-0.0283146774216-0.0451085739102-0.135323554830.0146328501910.1717569303010.02241576761950.2147398026390.03332638708320.006868799153970.122283387842-0.003562608608720.1535644760126.591776795427.033308479810.6991309506
30.509602959202-1.00541831681.163482131897.21886262932-3.434860763833.34101315149-0.0380727536096-0.289523083373-0.119437518630.8733205862110.2738036927570.225409282125-0.268854260083-0.107599545594-0.1882377311350.3048503033470.02528473644250.05554734302140.349302474957-0.02743920887770.31403393582139.354617687515.49364353928.59875810363
42.00862725018-0.664702032087-0.200296162652.475881020830.7919583164663.127951960520.08626583350490.1669630039810.136743311731-0.3280935083870.0524534637347-0.08248760304-0.2884671729180.193581504639-0.1133770095250.3086389812260.004014898434250.01639429751430.1550257005060.01508843283710.14186552787928.90216567237.92824933834.31627180639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 167 )

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