+Open data
-Basic information
Entry | Database: PDB / ID: 3rzu | ||||||
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Title | The Crystal Structure of the Catalytic Domain of AMSH | ||||||
Components | STAM-binding protein | ||||||
Keywords | HYDROLASE / Ubiquitin Hydrolase / STAM / Endosome-associated deubiquitinating enzyme | ||||||
Function / homology | Function and homology information negative regulation of hippocampal neuron apoptotic process / hippocampal neuron apoptotic process / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / deubiquitinase activity / negative regulation of Ras protein signal transduction / metal-dependent deubiquitinase activity / K63-linked deubiquitinase activity / protein deubiquitination / cell surface receptor signaling pathway via JAK-STAT / cleavage furrow ...negative regulation of hippocampal neuron apoptotic process / hippocampal neuron apoptotic process / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / deubiquitinase activity / negative regulation of Ras protein signal transduction / metal-dependent deubiquitinase activity / K63-linked deubiquitinase activity / protein deubiquitination / cell surface receptor signaling pathway via JAK-STAT / cleavage furrow / mitotic cytokinesis / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Metalloprotease DUBs / early endosome / endosome / protein domain specific binding / positive regulation of cell population proliferation / proteolysis / extracellular exosome / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Davies, C.W. / Das, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Structural and Thermodynamic Comparison of the Catalytic Domain of AMSH and AMSH-LP: Nearly Identical Fold but Different Stability. Authors: Davies, C.W. / Paul, L.N. / Kim, M.I. / Das, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rzu.cif.gz | 484.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rzu.ent.gz | 401.3 KB | Display | PDB format |
PDBx/mmJSON format | 3rzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rzu_validation.pdf.gz | 489.8 KB | Display | wwPDB validaton report |
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Full document | 3rzu_full_validation.pdf.gz | 504.5 KB | Display | |
Data in XML | 3rzu_validation.xml.gz | 45.8 KB | Display | |
Data in CIF | 3rzu_validation.cif.gz | 61.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/3rzu ftp://data.pdbj.org/pub/pdb/validation_reports/rz/3rzu | HTTPS FTP |
-Related structure data
Related structure data | 3rzvC 2znrS 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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Unit cell |
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-Components
#1: Protein | Mass: 20616.455 Da / Num. of mol.: 7 / Fragment: Catalytic Domain, residues 243-424 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMSH, STAMBP, STAMBP (AMSH) / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: O95630, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases #2: Chemical | ChemComp-ZN / #3: 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: 2.48 Å3/Da / Density % sol: 50.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M Sodium malonate, 20% PEG 3350, 5% PEG 400, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 10, 2010 / Details: Mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. all: 49199 / Num. obs: 48953 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 47.5 Å2 / Rsym value: 0.085 / Net I/σ(I): 12.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZNR Resolution: 2.5→47.152 Å / SU ML: 0.57 / σ(F): 1.34 / Phase error: 24.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.664 Å2 / ksol: 0.334 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→47.152 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 33.5007 Å / Origin y: 9.6836 Å / Origin z: 18.7944 Å
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Refinement TLS group | Selection details: all |