+Open data
-Basic information
Entry | Database: PDB / ID: 1m61 | ||||||
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Title | Crystal structure of the apo SH2 domains of ZAP-70 | ||||||
Components | TYROSINE-PROTEIN KINASE ZAP-70 | ||||||
Keywords | TRANSFERASE / apo form | ||||||
Function / homology | Function and homology information T cell aggregation / T cell migration / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / positive thymic T cell selection / beta selection / positive regulation of alpha-beta T cell differentiation / positive regulation of T cell differentiation / T cell receptor complex / B cell activation ...T cell aggregation / T cell migration / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / positive thymic T cell selection / beta selection / positive regulation of alpha-beta T cell differentiation / positive regulation of T cell differentiation / T cell receptor complex / B cell activation / Translocation of ZAP-70 to Immunological synapse / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / positive regulation of calcium-mediated signaling / extrinsic component of cytoplasmic side of plasma membrane / phosphotyrosine residue binding / T cell activation / calcium-mediated signaling / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / cell-cell junction / T cell receptor signaling pathway / protein tyrosine kinase activity / adaptive immune response / cell differentiation / intracellular signal transduction / immune response / signaling receptor binding / protein phosphorylation / innate immune response / ATP binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Folmer, R.H.A. / Geschwindner, S. / Xue, Y. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystal structure and NMR studies of the apo SH2 domains of ZAP-70: two bikes rather than a tandem Authors: Folmer, R.H.A. / Geschwindner, S. / Xue, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m61.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m61.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 1m61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/1m61 ftp://data.pdbj.org/pub/pdb/validation_reports/m6/1m61 | HTTPS FTP |
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-Related structure data
Related structure data | 1a81S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29276.547 Da / Num. of mol.: 1 / Fragment: tandem SH2 domains (Residues 1-256) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P43403, EC: 2.7.1.112 |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.13 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG3350, Sodium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0158 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 6, 1999 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0158 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 9435 / Num. obs: 9426 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Biso Wilson estimate: 43.9 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.062 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1360 / Rsym value: 0.456 / % possible all: 97.8 |
Reflection | *PLUS Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS Lowest resolution: 2.63 Å / % possible obs: 97.8 % / Rmerge(I) obs: 0.456 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1A81 Resolution: 2.5→18.85 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 591220.75 / Data cutoff high rms absF: 591220.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.0604 Å2 / ksol: 0.311367 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→18.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / % reflection Rfree: 4 % / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.246 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.61 Å / Num. reflection Rfree: 47 / Rfactor Rwork: 0.344 / Num. reflection Rwork: 1148 |