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- PDB-7moi: Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypica... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7moi | ||||||
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Title | Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in complex with Phenyl Phosphate | ||||||
![]() | Tyrosine-protein phosphatase DSP1 | ||||||
![]() | HYDROLASE / inositol / inositol pyrophosphate / TRANSFERASE / cell-signaling / phosphatase / substrate recognition / reaction mechanism / intermediate / phosphate / metaphosphate / molecular dynamic simulation / self-activation / catalytic water | ||||||
Function / homology | ![]() inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / diphosphoinositol-polyphosphate diphosphatase / phosphatase activity / protein tyrosine phosphatase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, H. / Shears, S.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A structural expose of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop. Authors: Wang, H. / Perera, L. / Jork, N. / Zong, G. / Riley, A.M. / Potter, B.V.L. / Jessen, H.J. / Shears, S.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.8 KB | Display | ![]() |
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PDB format | ![]() | 121.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7modC ![]() 7moeC ![]() 7mofC ![]() 7mogC ![]() 7mohC ![]() 7mojC ![]() 7mokC ![]() 7molC ![]() 7momC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 19642.770 Da / Num. of mol.: 2 / Mutation: C150S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.12 Å3/Da / Density % sol: 70.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.4 M NaCl, 100 mM HEPES PH 7.2, 50 mM beta-mercaptoethanol at 298K (3 ul of 5.5 mg/ml protein plus 1 ul of well buffer in the crystallization drop). The formed crystal was soaked in 30% ...Details: 0.4 M NaCl, 100 mM HEPES PH 7.2, 50 mM beta-mercaptoethanol at 298K (3 ul of 5.5 mg/ml protein plus 1 ul of well buffer in the crystallization drop). The formed crystal was soaked in 30% PEG400, 13mM MgCl2, 33mM NaF, 50 mM beta-mercaptoethanol, 66 mM HEPES, pH 7.2, and 10 mM phenyl phosphate for 4 days. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 59714 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rrim(I) all: 0.04 / Net I/σ(I): 49.6 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2944 / Rrim(I) all: 0.931 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.12 Å2 / Biso mean: 26.305 Å2 / Biso min: 10.23 Å2
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Refinement step | Cycle: final / Resolution: 1.8→37.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.849 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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