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Yorodumi- PDB-6apx: Crystal structure of human dual specificity phosphatase 1 catalyt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6apx | ||||||
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Title | Crystal structure of human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion in complex with the monobody YSX1 | ||||||
Components |
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Keywords | HYDROLASE / Dual specificity phosphatase / DUSP / C258S | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.491 Å | ||||||
Authors | Gumpena, R. / Lountos, G.T. / Sreejith, R.K. / Tropea, J.E. / Cherry, S. / Waugh, D.S. | ||||||
Citation | Journal: Protein Sci. / Year: 2018 Title: Crystal structure of the human dual specificity phosphatase 1 catalytic domain. Authors: Gumpena, R. / Lountos, G.T. / Raran-Kurussi, S. / Tropea, J.E. / Cherry, S. / 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 | 6apx.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6apx.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 6apx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/6apx ftp://data.pdbj.org/pub/pdb/validation_reports/ap/6apx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57103.613 Da / Num. of mol.: 1 Mutation: D82A, K83A, E172A, N173A, K239A, K362A, E359A, D363A, C258S Source method: isolated from a genetically manipulated source Details: P0AEX9 residues 27-392, P28562-1 residues 172-314 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: 10415.582 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) | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67.29 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: 75 mM MES pH 5.9 2.4 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 8, 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: 2.49→50 Å / Num. obs: 36681 / % possible obs: 99.7 % / Redundancy: 17.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 40.1 |
Reflection shell | Resolution: 2.49→2.53 Å / Redundancy: 9 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / Num. unique obs: 1728 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H4Z, 3CSB, 3EZZ Resolution: 2.491→37.268 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.491→37.268 Å
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Refine LS restraints |
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LS refinement shell |
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