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Yorodumi- PDB-6d65: Crystal structure of the human dual specificity phosphatase 1 cat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d65 | ||||||
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Title | Crystal structure of the human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion in complex with the designed AR protein off7 | ||||||
Components |
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Keywords | HYDROLASE / Dual specificity phosphatase / 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 / 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 / detection of maltose stimulus / protein serine/threonine phosphatase activity / maltose transport complex / protein-serine/threonine phosphatase / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / peptidyl-tyrosine dephosphorylation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / protein-tyrosine-phosphatase / 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 | Escherichia coli (E. coli) Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.348 Å | ||||||
Authors | Gumpena, R. / Lountos, G.T. / Waugh, D.S. | ||||||
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 | 6d65.cif.gz | 283.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d65.ent.gz | 225.3 KB | Display | PDB format |
PDBx/mmJSON format | 6d65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/6d65 ftp://data.pdbj.org/pub/pdb/validation_reports/d6/6d65 | HTTPS FTP |
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-Related structure data
Related structure data | 6d66C 6d67C 1svxS 3ezzS 3h4zS 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 57103.613 Da / Num. of mol.: 2 Mutation: 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 #2: Protein | Mass: 18308.467 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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-Non-polymers , 4 types, 656 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EOH / #6: 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: 2.99 Å3/Da / Density % sol: 58.84 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.15 M NaCl 0.1 M sodium cacodylate 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→50 Å / Num. obs: 75855 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.34→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3726 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H4Z, 3EZZ, 1SVX Resolution: 2.348→38.675 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.348→38.675 Å
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Refine LS restraints |
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LS refinement shell |
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