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- PDB-7mod: 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: 7mod | ||||||
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Title | Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in Complex with Phosphate in Conformation A (Pi(A)) | ||||||
![]() | 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 | ![]() phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / 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 | ![]() | 170.4 KB | Display | ![]() |
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PDB format | ![]() | 134.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7moeC ![]() 7mofC ![]() 7mogC ![]() 7mohC ![]() 7moiC ![]() 7mojC ![]() 7mokC ![]() 7molC ![]() 7momC ![]() 1xriS S: Starting model for refinement 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: 4.18 Å3/Da / Density % sol: 70.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.4 M NaCl, 100 mM HEPES pH7.2, 50 mM beta-mercaptoethanol at 298K (3 ul of 5.5 mg/ml protein plus 1 ul of well buffer in the crystallization drop). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 74329 / % possible obs: 99.6 % / Redundancy: 7.8 % / Rrim(I) all: 0.076 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.65→1.69 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5335 / Rrim(I) all: 0.849 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1XRI Resolution: 1.65→44.36 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.02 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 343.37 Å2 / Biso mean: 20.841 Å2 / Biso min: 5.27 Å2
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Refinement step | Cycle: final / Resolution: 1.65→44.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.651→1.694 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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