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- PDB-1bkl: SELF-ASSOCIATED APO SRC SH2 DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1bkl
TitleSELF-ASSOCIATED APO SRC SH2 DOMAIN
ComponentsPP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN
KeywordsV-SRC SH2 DOMAIN / PHOSPHOTYROSINE RECOGNITION DOMAIN / PP60 SRC SH2 DOMAIN
Function / homology
Function and homology information


non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / phosphorylation / ATP binding
Similarity search - Function
SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily ...SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase transforming protein Src
Similarity search - Component
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHolland, D.R. / Rubin, J.R.
Citation
Journal: To be Published
Title: Novel Pp60Src Sh2 Domain Crystal Structures: A 2.0 Angstrom Co-Crystal Structure of a D-Amino Acid Substituted Phosphopeptide Complex and a 2.1 Angstrom Apo Structure Displaying Self-Association
Authors: Holland, D.R. / Lunney, E.A. / Plummer, M.S. / Mueller, W.T. / Mcconnell, P. / Pavlovsky, A. / Para, K.S. / Shahripour, A. / Humblet, C. / Sawyer, T.K. / Rubin, J.R.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: Binding of a High Affinity Phosphotyrosyl Peptide to the Src Sh2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms
Authors: Waksman, G. / Shoelson, S.E. / Pant, N. / Cowburn, D. / Kuriyan, J.
History
DepositionMay 2, 1997Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,8371
Polymers12,8371
Non-polymers00
Water70339
1
A: PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN

A: PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN


Theoretical massNumber of molelcules
Total (without water)25,6752
Polymers25,6752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)60.200, 71.900, 34.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN / SRC SH2


Mass: 12837.392 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN
Mutation: INS(GS) AT N-TERMINUS, INS(EFIVTD) AT C-TERMINUS, BYPRODUCT OF CLONING
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / Strain: SCHMIDT-RUPPIN STRAIN A / Production host: Escherichia coli (E. coli) / Strain (production host): JM 83 / References: UniProt: P00524, EC: 2.7.1.112
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsG-S ARE NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING E-F-I-V-T-D NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING

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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: 2.9 Å3/Da / Density % sol: 57.82 % / Description: WAKSMAN AND KURIYAN SRC SH2 STRUCTURE
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.6
Details: 2M AMMONIUM SULFATE PH 6.6 , 25 MG/ML SRC SH2, SITTING DROPS, vapor diffusion - sitting drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.34
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1994
RadiationMonochromator: CU FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 6947 / % possible obs: 83.2 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5 / % possible all: 70.9

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
XDSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PROTEIN MODEL FROM 1SPS

1sps


Resolution: 2.1→8 Å / Cross valid method: R-FREE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.304 415 10 %RANDOM
Rwork0.2 ---
obs0.2 4351 63 %-
Displacement parametersBiso mean: 24.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 0 39 919
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.3 29
Rwork0.29 220

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