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Yorodumi- PDB-7l97: Crystal structure of STAMBPL1 in complex with an engineered binder -
+Open data
-Basic information
Entry | Database: PDB / ID: 7l97 | ||||||
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Title | Crystal structure of STAMBPL1 in complex with an engineered binder | ||||||
Components |
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Keywords | PROTEIN BINDING / STAMBP1 / Ubv / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / cellular response to L-leucine / metal-dependent deubiquitinase activity / K63-linked deubiquitinase activity / positive regulation of TORC1 signaling / Metalloprotease DUBs / endosome / proteolysis / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å | ||||||
Authors | Guo, Y. / Dong, A. / Hou, F. / Li, Y. / Zhang, W. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Structural and functional characterization of ubiquitin variant inhibitors for the JAMM-family deubiquitinases STAMBP and STAMBPL1. Authors: Guo, Y. / Liu, Q. / Mallette, E. / Caba, C. / Hou, F. / Fux, J. / LaPlante, G. / Dong, A. / Zhang, Q. / Zheng, H. / Tong, Y. / Zhang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l97.cif.gz | 67.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l97.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 7l97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7l97_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 7l97_full_validation.pdf.gz | 435 KB | Display | |
Data in XML | 7l97_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 7l97_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/7l97 ftp://data.pdbj.org/pub/pdb/validation_reports/l9/7l97 | HTTPS FTP |
-Related 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: 19649.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STAMBPL1, AMSHLP, KIAA1373 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q96FJ0, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases |
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#2: Protein | Mass: 8780.866 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 5 types, 69 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.19 Å3/Da / Density % sol: 43.78 % / Mosaicity: 2.773 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG 1500, 0.2M NaCl, 0.1M HEPES pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 23, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 16078 / % possible obs: 99 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.063 / Rrim(I) all: 0.139 / Χ2: 0.994 / Net I/σ(I): 7.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZNR,1UBQ Resolution: 2.01→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.954 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.03 Å2 / Biso mean: 37.279 Å2 / Biso min: 22.79 Å2
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Refinement step | Cycle: final / Resolution: 2.01→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.014→2.066 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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