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Yorodumi- PDB-6d66: Crystal structure of the human dual specificity 1 catalytic domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d66 | ||||||
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Title | Crystal structure of the human dual specificity 1 catalytic domain (C258S) as a maltose binding protein fusion in complex with the designed AR protein mbp3_16 | ||||||
Components |
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Keywords | HYDROLASE / DUSP / C258S / MBP / DARPin | ||||||
Function / homology | Function and homology information negative regulation of monocyte chemotaxis / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / endoderm formation / regulation of mitotic cell cycle spindle assembly checkpoint / negative regulation of p38MAPK cascade / negative regulation of meiotic cell cycle / 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 / regulation of mitotic cell cycle spindle assembly checkpoint / negative regulation of p38MAPK cascade / negative regulation of meiotic cell cycle / 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 / myosin phosphatase activity / protein serine/threonine phosphatase activity / detection of maltose stimulus / maltose binding / negative regulation of MAPK cascade / maltose transport complex / protein-serine/threonine phosphatase / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / peptidyl-tyrosine dephosphorylation / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / negative regulation of MAP kinase activity / protein-tyrosine-phosphatase / 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 | Escherichia coli (E. coli) Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.226 Å | ||||||
Authors | Gumpena, R. / Waugh, D.S. / Lountos, G.T. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d66.cif.gz | 151.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d66.ent.gz | 115.2 KB | Display | PDB format |
PDBx/mmJSON format | 6d66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/6d66 ftp://data.pdbj.org/pub/pdb/validation_reports/d6/6d66 | HTTPS FTP |
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-Related structure data
Related structure data | 6d65SC 6d67C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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, E362A, D363A, C258S,D82A, K83A, E172A, N173A, K239A, E362A, D363A, C258S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human) Strain: K12 / Gene: malE, b4034, JW3994, DUSP1, CL100, MKP1, PTPN10, VH1 / Production host: Escherichia coli BL21(DE3) (bacteria) 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: Escherichia coli BL21(DE3) (bacteria) |
-Non-polymers , 8 types, 331 molecules
#3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-PG4 / | #9: Chemical | ChemComp-DAL / | #10: 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: 2.96 Å3/Da / Density % sol: 58.38 % |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 11, 2016 |
Radiation | Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→50 Å / Num. obs: 43247 / % possible obs: 98.6 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 46.4 |
Reflection shell | Resolution: 2.22→2.3 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 3697 / % possible all: 86.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6D65 Resolution: 2.226→36.444 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.226→36.444 Å
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Refine LS restraints |
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LS refinement shell |
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