- PDB-3syx: Crystal Structure of the WH1 domain from human sprouty-related, E... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3syx
Title
Crystal Structure of the WH1 domain from human sprouty-related, EVH1 domain-containing protein. Northeast Structural Genomics Consortium Target HR5538B.
Components
Sprouty-related, EVH1 domain-containing protein 1
Keywords
SIGNALING PROTEIN / WH1 domain / Human sprouty-related / EVH1 domain-containing protein / Q7Z699 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / PSI-Biology
Function / homology
Function and homology information
regulation of protein deacetylation / negative regulation of lens fiber cell differentiation / stem cell factor receptor binding / FGFRL1 modulation of FGFR1 signaling / positive regulation of DNA damage response, signal transduction by p53 class mediator / vasculogenesis involved in coronary vascular morphogenesis / negative regulation of cell migration involved in sprouting angiogenesis / protein serine/threonine kinase inhibitor activity / negative regulation of epithelial to mesenchymal transition / negative regulation of MAPK cascade ...regulation of protein deacetylation / negative regulation of lens fiber cell differentiation / stem cell factor receptor binding / FGFRL1 modulation of FGFR1 signaling / positive regulation of DNA damage response, signal transduction by p53 class mediator / vasculogenesis involved in coronary vascular morphogenesis / negative regulation of cell migration involved in sprouting angiogenesis / protein serine/threonine kinase inhibitor activity / negative regulation of epithelial to mesenchymal transition / negative regulation of MAPK cascade / negative regulation of peptidyl-threonine phosphorylation / regulation of MAPK cascade / RAS signaling downstream of NF1 loss-of-function variants / phosphatase binding / negative regulation of angiogenesis / caveola / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / Regulation of RAS by GAPs / protein kinase binding / nucleoplasm / plasma membrane / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal grow
Temperature: 277 K / Method: microbatch crystallization under oil / pH: 6 Details: 12% PEG 20000, 0.1 M potassium acetate, 10 mM yttrium(III) chloride, 0.1 M MES, pH 6.0, Microbatch crystallization under oil, temperature 277K
Resolution: 2.453→26.377 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 27.8 / Stereochemistry target values: ML Details: There is a yttrium atom located in special position with occupancy 0.5.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.271
650
4.7 %
RANDOM
Rwork
0.228
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obs
0.23
13821
99.54 %
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Solvent computation
Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.482 Å2 / ksol: 0.317 e/Å3
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