+Open data
-Basic information
Entry | Database: PDB / ID: 7w3u | |||||||||
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Title | USP34 catalytic domain in complex with UbPA | |||||||||
Components |
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Keywords | HYDROLASE / USP34 in complex | |||||||||
Function / homology | Function and homology information protein K48-linked deubiquitination / protein deubiquitination / TCF dependent signaling in response to WNT / Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity ...protein K48-linked deubiquitination / protein deubiquitination / TCF dependent signaling in response to WNT / Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å | |||||||||
Authors | Xu, G.L. / Ming, Z.H. | |||||||||
Funding support | 2items
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Citation | Journal: J.Mol.Biol. / Year: 2022 Title: Structural Insights into the Catalytic Mechanism and Ubiquitin Recognition of USP34. Authors: Xu, G. / Su, H. / Lu, L. / Liu, X. / Zhao, L. / Tang, B. / Ming, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w3u.cif.gz | 514.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w3u.ent.gz | 429.8 KB | Display | PDB format |
PDBx/mmJSON format | 7w3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w3u_validation.pdf.gz | 484.3 KB | Display | wwPDB validaton report |
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Full document | 7w3u_full_validation.pdf.gz | 511.3 KB | Display | |
Data in XML | 7w3u_validation.xml.gz | 46 KB | Display | |
Data in CIF | 7w3u_validation.cif.gz | 61.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/7w3u ftp://data.pdbj.org/pub/pdb/validation_reports/w3/7w3u | HTTPS FTP |
-Related structure data
Related structure data | 7w3rSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 44897.805 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP34, KIAA0570, KIAA0729 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q70CQ2, ubiquitinyl hydrolase 1 #2: Protein | Mass: 8519.778 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: J3QS39 #3: Chemical | #4: 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: 2.39 Å3/Da / Density % sol: 48.46 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 15% w/v PEG 3350, 0.8M Magnesium chloride hexahydrate, 0.6mM Lyso PG, 1 mM Facade R-EPC |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 3.13→23.596 Å / Num. obs: 27763 / % possible obs: 99.62 % / Redundancy: 15.21 % / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 3.13→3.242 Å / CC1/2: 0.721 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7W3R Resolution: 3.13→23.596 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.13 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 186.28 Å2 / Biso mean: 70 Å2 / Biso min: 48.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.13→23.596 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 25.9224 Å / Origin y: 48.5643 Å / Origin z: 17.549 Å
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Refinement TLS group |
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