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- PDB-5kaz: Human SH2D1B structure -

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Basic information

Entry
Database: PDB / ID: 5kaz
TitleHuman SH2D1B structure
ComponentsSH2 domain-containing protein 1B
KeywordsSIGNALING PROTEIN / SH2D1B / EAT2 / SLAM / SAP
Function / homology
Function and homology information


positive regulation of natural killer cell mediated immunity / leukocyte activation involved in immune response / positive regulation of innate immune response / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / protein-macromolecule adaptor activity / adaptive immune response / innate immune response / cytosol
Similarity search - Function
EAT-2, SH2 domain / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SH2 domain-containing protein 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsTaha, M. / Nezerwa, E. / Nam, H.-J.
CitationJournal: Protein Pept. Lett. / Year: 2016
Title: The X-ray Crystallographic Structure of Human EAT2 (SH2D1B).
Authors: Taha, M. / Nezerwa, E. / Nam, H.J.
History
DepositionJun 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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: SH2 domain-containing protein 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1942
Polymers12,0981
Non-polymers961
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.983, 66.983, 105.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-425-

HOH

31A-433-

HOH

41A-444-

HOH

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Components

#1: Protein SH2 domain-containing protein 1B / EWS/FLI1-activated transcript 2 / EAT-2


Mass: 12098.149 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SH2D1B, EAT2 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O14796
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Na-Citrate pH 5.5, 24% PEG 4000, 50 mM (NH)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→31.054 Å / Num. obs: 13571 / % possible obs: 98.8 % / Redundancy: 4.1 % / Net I/σ(I): 33.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
RefinementResolution: 1.7→35.191 Å / SU ML: 0.14 / σ(F): 1.5 / Phase error: 22.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 652 4.88 %
Rwork0.1894 --
obs0.1907 13365 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→35.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 10 282 1978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007866
X-RAY DIFFRACTIONf_angle_d1.2091166
X-RAY DIFFRACTIONf_dihedral_angle_d12.853336
X-RAY DIFFRACTIONf_chiral_restr0.045126
X-RAY DIFFRACTIONf_plane_restr0.005147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6999-1.83120.25651090.19772510X-RAY DIFFRACTION99
1.8312-2.01540.24171360.19832498X-RAY DIFFRACTION99
2.0154-2.3070.22641160.19172551X-RAY DIFFRACTION99
2.307-2.90640.20061390.21562534X-RAY DIFFRACTION99
2.9064-35.19820.20831520.17452620X-RAY DIFFRACTION97

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