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Open data
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Basic information
Entry | Database: PDB / ID: 1rpm | ||||||
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Title | HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE MU, DOMAIN 1 | ||||||
![]() | RECEPTOR PROTEIN TYROSINE PHOSPHATASE MU | ||||||
![]() | RECEPTOR / PHOSPHATASE / SIGNAL TRANSDUCTION / ADHESION / HYDROLASE | ||||||
Function / homology | ![]() retina layer formation / transmembrane receptor protein tyrosine phosphatase activity / negative regulation of endothelial cell migration / retinal ganglion cell axon guidance / negative regulation of endothelial cell proliferation / phosphatase activity / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of angiogenesis / protein dephosphorylation / protein-tyrosine-phosphatase ...retina layer formation / transmembrane receptor protein tyrosine phosphatase activity / negative regulation of endothelial cell migration / retinal ganglion cell axon guidance / negative regulation of endothelial cell proliferation / phosphatase activity / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of angiogenesis / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / adherens junction / neuron projection development / cell-cell junction / lamellipodium / response to xenobiotic stimulus / cadherin binding / perinuclear region of cytoplasm / signal transduction / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hoffmann, K.M.V. / Tonks, N.K. / Barford, D. | ||||||
![]() | ![]() Title: The crystal structure of domain 1 of receptor protein-tyrosine phosphatase mu. Authors: Hoffmann, K.M. / Tonks, N.K. / Barford, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.6 KB | Display | ![]() |
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PDB format | ![]() | 99.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.6 KB | Display | ![]() |
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Full document | ![]() | 426.7 KB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 36.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yfoS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.0988, -0.0011, 0.9951), Vector: |
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Components
#1: Protein | Mass: 32151.496 Da / Num. of mol.: 2 / Fragment: CYTOSOLIC MEMBRANE PROXIMAL CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 Details: PROTEIN WAS CRYSTALLIZED FROM 750 MM SODIUM CITRATE, PH 5.5, 2 MM DTT, 0.5 MM EDTA | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1997 |
Radiation | Monochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→15 Å / Num. obs: 26733 / % possible obs: 90 % / Redundancy: 4 % / Rsym value: 0.029 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Rsym value: 0.064 / % possible all: 92 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 112065 / Rmerge(I) obs: 0.03 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1YFO Resolution: 2.3→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: FREE R / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→8 Å / Total num. of bins used: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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