+Open data
-Basic information
Entry | Database: PDB / ID: 1rpm | ||||||
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Title | HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE MU, DOMAIN 1 | ||||||
Components | RECEPTOR PROTEIN TYROSINE PHOSPHATASE MU | ||||||
Keywords | RECEPTOR / PHOSPHATASE / SIGNAL TRANSDUCTION / ADHESION / HYDROLASE | ||||||
Function / homology | Function and homology information retina layer formation / transmembrane receptor protein tyrosine phosphatase activity / negative regulation of endothelial cell migration / retinal ganglion cell axon guidance / intracellular non-membrane-bounded organelle / negative regulation of endothelial cell proliferation / homophilic cell adhesion via plasma membrane adhesion molecules / phosphatase activity / negative regulation of angiogenesis / protein dephosphorylation ...retina layer formation / transmembrane receptor protein tyrosine phosphatase activity / negative regulation of endothelial cell migration / retinal ganglion cell axon guidance / intracellular non-membrane-bounded organelle / negative regulation of endothelial cell proliferation / homophilic cell adhesion via plasma membrane adhesion molecules / phosphatase activity / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hoffmann, K.M.V. / Tonks, N.K. / Barford, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1997 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rpm.cif.gz | 124.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rpm.ent.gz | 99.2 KB | Display | PDB format |
PDBx/mmJSON format | 1rpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/1rpm ftp://data.pdbj.org/pub/pdb/validation_reports/rp/1rpm | HTTPS FTP |
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-Related structure data
Related structure data | 1yfoS 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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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: |
-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.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P28827, protein-tyrosine-phosphatase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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