+Open data
-Basic information
Entry | Database: PDB / ID: 7lm3 | ||||||
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Title | Crystal Structure of Thr316Ala mutant of JAMM domain of S. pombe | ||||||
Components | AMSH-like protease sst2 | ||||||
Keywords | METAL BINDING PROTEIN / Deubiquitinating enzymes / JAMM domain / ESCRT complexes / Lus63-linked polyubiquitin chains | ||||||
Function / homology | Function and homology information Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / late endosome to vacuole transport / metal-dependent deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / K63-linked deubiquitinase activity / cell division site ...Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / late endosome to vacuole transport / metal-dependent deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / K63-linked deubiquitinase activity / cell division site / ubiquitin binding / endosome / zinc ion binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Shrestha, R. / Das, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2021 Title: Crystal structure of the Thr316Ala mutant of a yeast JAMM deubiquitinase: implication of active-site loop dynamics in catalysis. Authors: Shrestha, R. / Das, C. #1: Journal: Biochemistry / Year: 2014 Title: Insights into the mechanism of deubiquitination by JAMM deubiquitinases from cocrystal structures of the enzyme with the substrate and product. Authors: Shrestha, R.K. / Ronau, J.A. / Davies, C.W. / Guenette, R.G. / Strieter, E.R. / Paul, L.N. / Das, C. #2: Journal: Biochemistry / Year: 2015 Title: Dynamics of an Active-Site Flap Contributes to Catalysis in a JAMM Family Metallo Deubiquitinase. Authors: Bueno, A.N. / Shrestha, R.K. / Ronau, J.A. / Babar, A. / Sheedlo, M.J. / Fuchs, J.E. / Paul, L.N. / Das, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lm3.cif.gz | 183.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lm3.ent.gz | 119.7 KB | Display | PDB format |
PDBx/mmJSON format | 7lm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lm3_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
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Full document | 7lm3_full_validation.pdf.gz | 448.2 KB | Display | |
Data in XML | 7lm3_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 7lm3_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/7lm3 ftp://data.pdbj.org/pub/pdb/validation_reports/lm/7lm3 | HTTPS FTP |
-Related structure data
Related structure data | 4jxeS S: Starting model for refinement |
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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
#1: Protein | Mass: 21951.707 Da / Num. of mol.: 2 / Mutation: T316A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: sst2, SPAC19B12.10 / Production host: Escherichia coli (E. coli) References: UniProt: Q9P371, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases #2: Chemical | ChemComp-ZN / #3: Chemical | Has ligand of interest | N | |
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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: 2.77 Å3/Da / Density % sol: 55.64 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium phosphate dibasic (pH 8.0), 20% w/v polyethylene glycol 3,350 with 40% v/v Polypropylene glycol P400 as an additive |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 12793 / % possible obs: 98.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.043 / Rrim(I) all: 0.086 / Χ2: 1.109 / Net I/σ(I): 9 / Num. measured all: 49946 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JXE Resolution: 2.7→44.04 Å / SU ML: 0.5618 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 32.4016 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.42 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→44.04 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: -29.3808393257 Å / Origin y: 19.8688518798 Å / Origin z: 12.6805998767 Å
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Refinement TLS group | Selection details: all |