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- PDB-6d67: Crystal structure of the human dual specificity phosphatase 1 cat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d67 | |||||||||
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Title | Crystal structure of the human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion (maltose bound form) in complex with the designed AR protein mbp3_16 | |||||||||
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![]() | HYDROLASE / Dual specificity phosphatase / DUSP / C258S / MBP / maltose / DARPin | |||||||||
Function / homology | ![]() negative regulation of monocyte chemotaxis / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / endoderm formation / negative regulation of p38MAPK cascade / negative regulation of meiotic cell cycle / regulation of mitotic cell cycle spindle assembly checkpoint / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation ...negative regulation of monocyte chemotaxis / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / endoderm formation / negative regulation of p38MAPK cascade / negative regulation of meiotic cell cycle / regulation of mitotic cell cycle spindle assembly checkpoint / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / protein tyrosine/serine/threonine phosphatase activity / RAF-independent MAPK1/3 activation / cellular response to chemokine / negative regulation of cell adhesion / mitogen-activated protein kinase binding / negative regulation of MAPK cascade / myosin phosphatase activity / protein serine/threonine phosphatase activity / detection of maltose stimulus / protein-serine/threonine phosphatase / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / peptidyl-tyrosine dephosphorylation / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / protein-tyrosine-phosphatase / cell chemotaxis / negative regulation of MAP kinase activity / protein tyrosine phosphatase activity / Negative regulation of MAPK pathway / outer membrane-bounded periplasmic space / periplasmic space / cell cycle / negative regulation of cell population proliferation / DNA damage response / membrane / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Gumpena, R. / Lountos, G.T. / Waugh, D.S. | |||||||||
![]() | ![]() Title: MBP-binding DARPins facilitate the crystallization of an MBP fusion protein. Authors: Gumpena, R. / Lountos, G.T. / Waugh, D.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.5 KB | Display | ![]() |
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PDB format | ![]() | 105.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 855.4 KB | Display | ![]() |
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Full document | ![]() | 859 KB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 33.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d65SC ![]() 6d66C ![]() 3mp6S 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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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 57103.613 Da / Num. of mol.: 1 Mutation: D82A, K83A, E172A, N173A, K239A, E359A, K362A, D363A,D82A, K83A, E172A, N173A, C258S, K239A, E359A, K362A, D363A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12 / Gene: malE, b4034, JW3994, DUSP1, CL100, MKP1, PTPN10, VH1 / Production host: ![]() ![]() References: UniProt: P0AEX9, UniProt: P28562, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase |
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#2: Protein | Mass: 14787.509 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
-Sugars , 1 types, 1 molecules
#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
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-Non-polymers , 4 types, 85 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-PEG / | ||
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#5: Chemical | ChemComp-PO4 / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.65 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M DL-GLUTAMIC ACID 0.2 M DL-ALANINE 0.2 M GLYCINE 0.2 M DL-LYSINE 0.2 M DL-SERINE 0.1 M TRIS; BICINE 25% MPD 25% PEG1000 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 5, 2016 |
Radiation | Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 22649 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 2 / Num. unique obs: 2139 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MP6, 6D65 Resolution: 2.55→38.574 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→38.574 Å
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Refine LS restraints |
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LS refinement shell |
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