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- PDB-1xba: Crystal structure of apo syk tyrosine kinase domain -

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Basic information

Entry
Database: PDB / ID: 1xba
TitleCrystal structure of apo syk tyrosine kinase domain
ComponentsTyrosine-protein kinase SYK
KeywordsTRANSFERASE / spleen typrosine kinase / active conformation / structural genomics / Structural GenomiX
Function / homology
Function and homology information


interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / positive regulation of interleukin-3 production / cellular response to lectin / B cell receptor complex / Toll-like receptor binding / regulation of platelet aggregation / positive regulation of alpha-beta T cell proliferation ...interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / positive regulation of interleukin-3 production / cellular response to lectin / B cell receptor complex / Toll-like receptor binding / regulation of platelet aggregation / positive regulation of alpha-beta T cell proliferation / serotonin secretion by platelet / leukocyte activation involved in immune response / neutrophil activation involved in immune response / lymph vessel development / positive regulation of mast cell degranulation / gamma-delta T cell differentiation / positive regulation of mast cell cytokine production / collagen-activated tyrosine kinase receptor signaling pathway / positive regulation of gamma-delta T cell differentiation / cell surface pattern recognition receptor signaling pathway / regulation of platelet activation / cell activation / beta selection / cellular response to molecule of fungal origin / FLT3 signaling through SRC family kinases / early phagosome / leukotriene biosynthetic process / regulation of phagocytosis / regulation of DNA-binding transcription factor activity / regulation of tumor necrosis factor-mediated signaling pathway / macrophage activation involved in immune response / interleukin-3-mediated signaling pathway / positive regulation of bone resorption / positive regulation of monocyte chemotactic protein-1 production / cellular response to lipid / Fc epsilon receptor (FCERI) signaling / Interleukin-2 signaling / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of alpha-beta T cell differentiation / blood vessel morphogenesis / positive regulation of cell adhesion mediated by integrin / positive regulation of B cell differentiation / leukocyte cell-cell adhesion / T cell receptor complex / mast cell degranulation / Dectin-2 family / positive regulation of interleukin-4 production / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / amyloid-beta clearance / positive regulation of interleukin-10 production / positive regulation of receptor internalization / FCGR activation / cellular response to low-density lipoprotein particle stimulus / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of type I interferon production / Role of phospholipids in phagocytosis / phosphatase binding / regulation of ERK1 and ERK2 cascade / phospholipase binding / GPVI-mediated activation cascade / Signaling by CSF3 (G-CSF) / positive regulation of superoxide anion generation / phosphotyrosine residue binding / neutrophil chemotaxis / positive regulation of interleukin-12 production / Integrin signaling / positive regulation of TORC1 signaling / FCERI mediated Ca+2 mobilization / SH2 domain binding / positive regulation of calcium-mediated signaling / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / peptidyl-tyrosine phosphorylation / B cell differentiation / animal organ morphogenesis / integrin-mediated signaling pathway / positive regulation of interleukin-8 production / B cell receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / apoptotic signaling pathway / negative regulation of inflammatory response to antigenic stimulus / positive regulation of protein-containing complex assembly / calcium-mediated signaling / Inactivation of CSF3 (G-CSF) signaling / Regulation of actin dynamics for phagocytic cup formation / platelet activation / receptor internalization / positive regulation of interleukin-6 production / CLEC7A (Dectin-1) signaling / integrin binding / cellular response to amyloid-beta / protein import into nucleus / positive regulation of tumor necrosis factor production / kinase activity
Similarity search - Function
Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / : / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain ...Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / : / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase SYK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAtwell, S. / Adams, J.M. / Badger, J. / Buchanan, M.D. / Feil, I.K. / Froning, K.J. / Gao, X. / Hendle, J. / Keegan, K. / Leon, B.C. ...Atwell, S. / Adams, J.M. / Badger, J. / Buchanan, M.D. / Feil, I.K. / Froning, K.J. / Gao, X. / Hendle, J. / Keegan, K. / Leon, B.C. / Muller-Deickmann, H.J. / Nienaber, V.L. / Noland, B.W. / Post, K. / Rajashankar, K.R. / Ramos, A. / Russell, M. / Burley, S.K. / Buchanan, S.G.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: A novel mode of Gleevec binding is revealed by the structure of spleen tyrosine kinase.
Authors: Atwell, S. / Adams, J.M. / Badger, J. / Buchanan, M.D. / Feil, I.K. / Froning, K.J. / Gao, X. / Hendle, J. / Keegan, K. / Leon, B.C. / Muller-Deickmann, H.J. / Nienaber, V.L. / Noland, B.W. ...Authors: Atwell, S. / Adams, J.M. / Badger, J. / Buchanan, M.D. / Feil, I.K. / Froning, K.J. / Gao, X. / Hendle, J. / Keegan, K. / Leon, B.C. / Muller-Deickmann, H.J. / Nienaber, V.L. / Noland, B.W. / Post, K. / Rajashankar, K.R. / Ramos, A. / Russell, M. / Burley, S.K. / Buchanan, S.G.
History
DepositionAug 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 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: Tyrosine-protein kinase SYK


Theoretical massNumber of molelcules
Total (without water)33,8841
Polymers33,8841
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.785, 84.721, 90.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosine-protein kinase SYK / Spleen tyrosine kinase


Mass: 33884.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYK / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43405, EC: 2.7.1.112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growpH: 8.5 / Details: 15% peg 3350, 100mM Tris HCl (pH 8.5)

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9794 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→30.861 Å / Num. all: 21184 / Num. obs: 21184 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC5refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.83 Å / σ(F): 0
RfactorNum. reflection
Rfree0.278 1092
Rwork0.231 -
obs-21182
Solvent computationSolvent model: Mask bulk solvent correction
Displacement parametersBiso mean: 33.853 Å2
Baniso -1Baniso -2Baniso -3
1--0.636 Å20 Å20 Å2
2---1.243 Å20 Å2
3---1.879 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 0 68 2136
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.017
X-RAY DIFFRACTIONr_angle_refined_deg1.584
X-RAY DIFFRACTIONr_chiral_restr0.124
X-RAY DIFFRACTIONr_gen_planes_other0.007
X-RAY DIFFRACTIONr_mcbond_it1.291
X-RAY DIFFRACTIONr_mcangle_it2.012
X-RAY DIFFRACTIONr_scbond_it2.692
X-RAY DIFFRACTIONr_scangle_it3.874

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