+Open data
-Basic information
Entry | Database: PDB / ID: 1bkl | ||||||
---|---|---|---|---|---|---|---|
Title | SELF-ASSOCIATED APO SRC SH2 DOMAIN | ||||||
Components | PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN | ||||||
Keywords | V-SRC SH2 DOMAIN / PHOSPHOTYROSINE RECOGNITION DOMAIN / PP60 SRC SH2 DOMAIN | ||||||
Function / homology | Function and homology information osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell adhesion ...osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell adhesion / phosphorylation / signaling receptor binding / innate immune response / ATP binding Similarity search - Function | ||||||
Biological species | Rous sarcoma virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Holland, 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bkl.cif.gz | 41 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bkl.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 1bkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/1bkl ftp://data.pdbj.org/pub/pdb/validation_reports/bk/1bkl | HTTPS FTP |
---|
-Related structure data
Related structure data | 1spsS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | 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 / |
Sequence details | G-S ARE NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING E-F-I-V-T-D NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.82 % / Description: WAKSMAN AND KURIYAN SRC SH2 STRUCTURE |
---|---|
Crystal grow | Method: 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 |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.34 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1994 |
Radiation | Monochromator: CU FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.1→2.2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5 / % possible all: 70.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PROTEIN MODEL FROM 1SPS Resolution: 2.1→8 Å / Cross valid method: R-FREE / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.19 Å / Total num. of bins used: 8 /
|