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- PDB-1k9a: Crystal structure analysis of full-length carboxyl-terminal Src k... -

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Basic information

Entry
Database: PDB / ID: 1k9a
TitleCrystal structure analysis of full-length carboxyl-terminal Src kinase at 2.5 A resolution
ComponentsCarboxyl-terminal Src kinase
KeywordsTRANSFERASE / carboxyl-terminal Src kinase / COOH-terminal Src kinase / Csk / Src / SFK / signal transduction / SH2 / SH3 / Src Homology / tyrosine kinase / cytoplasmic tyrosine kinase / Cbp / oncogene / cancer
Function / homology
Function and homology information


GAB1 signalosome / Co-inhibition by PD-1 / Phosphorylation of CD3 and TCR zeta chains / Integrin signaling / negative regulation of Golgi to plasma membrane protein transport / RHOH GTPase cycle / regulation of Fc receptor mediated stimulatory signaling pathway / MAP2K and MAPK activation / negative regulation of low-density lipoprotein particle clearance / adherens junction organization ...GAB1 signalosome / Co-inhibition by PD-1 / Phosphorylation of CD3 and TCR zeta chains / Integrin signaling / negative regulation of Golgi to plasma membrane protein transport / RHOH GTPase cycle / regulation of Fc receptor mediated stimulatory signaling pathway / MAP2K and MAPK activation / negative regulation of low-density lipoprotein particle clearance / adherens junction organization / proline-rich region binding / negative regulation of bone resorption / cellular response to peptide hormone stimulus / negative regulation of phagocytosis / protein kinase A catalytic subunit binding / oligodendrocyte differentiation / negative regulation of interleukin-6 production / protein tyrosine kinase binding / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / negative regulation of ERK1 and ERK2 cascade / cell-cell junction / protein tyrosine kinase activity / protein phosphatase binding / adaptive immune response / negative regulation of cell population proliferation / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
CSK-like, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...CSK-like, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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 / Roll / 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 Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase CSK
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5 Å
AuthorsOgawa, A. / Takayama, Y. / Nagata, A. / Chong, K.T. / Takeuchi, S. / Sakai, H. / Nakagawa, A. / Nada, S. / Okada, M. / Tsukihara, T.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure of the carboxyl-terminal Src kinase, Csk.
Authors: Ogawa, A. / Takayama, Y. / Sakai, H. / Chong, K.T. / Takeuchi, S. / Nakagawa, A. / Nada, S. / Okada, M. / Tsukihara, T.
History
DepositionOct 28, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxyl-terminal Src kinase
B: Carboxyl-terminal Src kinase
C: Carboxyl-terminal Src kinase
D: Carboxyl-terminal Src kinase
E: Carboxyl-terminal Src kinase
F: Carboxyl-terminal Src kinase


Theoretical massNumber of molelcules
Total (without water)304,8796
Polymers304,8796
Non-polymers00
Water7,710428
1
A: Carboxyl-terminal Src kinase


Theoretical massNumber of molelcules
Total (without water)50,8131
Polymers50,8131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carboxyl-terminal Src kinase


Theoretical massNumber of molelcules
Total (without water)50,8131
Polymers50,8131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Carboxyl-terminal Src kinase


Theoretical massNumber of molelcules
Total (without water)50,8131
Polymers50,8131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Carboxyl-terminal Src kinase


Theoretical massNumber of molelcules
Total (without water)50,8131
Polymers50,8131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Carboxyl-terminal Src kinase


Theoretical massNumber of molelcules
Total (without water)50,8131
Polymers50,8131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Carboxyl-terminal Src kinase


Theoretical massNumber of molelcules
Total (without water)50,8131
Polymers50,8131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
C: Carboxyl-terminal Src kinase

D: Carboxyl-terminal Src kinase


Theoretical massNumber of molelcules
Total (without water)101,6262
Polymers101,6262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area3170 Å2
ΔGint-21 kcal/mol
Surface area41390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.000, 162.600, 232.400
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
Carboxyl-terminal Src kinase / Tyrosine-protein kinase CSK


Mass: 50813.219 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P32577, EC: 2.7.1.112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.56 Å3/Da / Density % sol: 65.47 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: ammonium sulphate, HEPES buffer, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
250 mMHEPES-NaOH1reservoirpH7.4
31.90-1.95 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD PX210 / Detector: CCD / Date: Jun 9, 2001
RadiationMonochromator: ROTATED-INCLINED SI(111) DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→73.5 Å / Num. all: 150489 / Num. obs: 150489 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 62.8 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 6.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 1.7 / Num. unique all: 17029 / % possible all: 98.2
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 73 Å
Reflection shell
*PLUS
% possible obs: 98.2 % / Num. unique obs: 17029

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXSphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.5→73.5 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2972 1.975 %RANDOM
Rwork0.246 ---
all0.246 150489 --
obs0.246 150489 --
Refine analyze
FreeObs
Luzzati coordinate error0.443 Å0.378 Å
Luzzati d res low-5 Å
Luzzati sigma a0.485 Å0.464 Å
Refinement stepCycle: LAST / Resolution: 2.5→73.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20885 0 0 428 21313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.427
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 2.5→2.52 Å / Rfactor Rfree error: 0.053
RfactorNum. reflection% reflection
Rfree0.41 58 -
Rwork0.36 --
obs-2660 87 %
Refinement
*PLUS
Lowest resolution: 73.5 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.41 / Rfactor Rwork: 0.36

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