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Yorodumi- PDB-6w2g: Crystal Structure of Y188G Variant of the Internal UBA Domain of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w2g | |||||||||
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Title | Crystal Structure of Y188G Variant of the Internal UBA Domain of HHR23A in Monoclinic Unit Cell | |||||||||
Components | UV excision repair protein RAD23 homolog A | |||||||||
Keywords | DNA BINDING PROTEIN / Ubiquitin Associated Domain / UBA Domain / Helical Bundle | |||||||||
Function / homology | Function and homology information regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome binding / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication / positive regulation of cell cycle / proteasome complex / Josephin domain DUBs / ubiquitin binding / nucleotide-excision repair ...regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome binding / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication / positive regulation of cell cycle / proteasome complex / Josephin domain DUBs / ubiquitin binding / nucleotide-excision repair / kinase binding / DNA Damage Recognition in GG-NER / protein destabilization / Formation of Incision Complex in GG-NER / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / single-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / intracellular membrane-bounded organelle / Golgi apparatus / protein-containing complex / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | |||||||||
Authors | Bowler, B.E. / Zeng, B. / Becht, D.C. / Rothfuss, M. / Sprang, S.R. / Mou, T.-C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: High-Accuracy Prediction of Stabilizing Surface Mutations to the Three-Helix Bundle, UBA(1), with EmCAST. Authors: Rothfuss, M.T. / Becht, D.C. / Zeng, B. / McClelland, L.J. / Yates-Hansen, C. / Bowler, B.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w2g.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w2g.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 6w2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w2g_validation.pdf.gz | 426 KB | Display | wwPDB validaton report |
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Full document | 6w2g_full_validation.pdf.gz | 426 KB | Display | |
Data in XML | 6w2g_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 6w2g_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/6w2g ftp://data.pdbj.org/pub/pdb/validation_reports/w2/6w2g | HTTPS FTP |
-Related 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: 5534.243 Da / Num. of mol.: 2 / Mutation: Y188G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAD23A / Plasmid: pGEX-2T Details (production host): Thrombin cleavage site replaced with TEV cleavage site Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54725 #2: Chemical | #3: Water | ChemComp-HOH / | 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: 1.76 Å3/Da / Density % sol: 29.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium sulfate, 0.1M Phosphate-citrate pH 4.2, 40%(v/v) Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→33.88 Å / Num. obs: 29568 / % possible obs: 94.77 % / Redundancy: 6.2 % / Biso Wilson estimate: 6.64 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01716 / Rpim(I) all: 0.007273 / Rrim(I) all: 0.01868 / Net I/σ(I): 56.13 |
Reflection shell | Resolution: 1.1→1.139 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.07858 / Mean I/σ(I) obs: 16.63 / Num. unique obs: 2513 / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.0396 / Rrim(I) all: 0.0884 / % possible all: 81.04 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: P43 UBA-1 Y188G Structure Solved by Sulfur SAD Resolution: 1.1→32.88 Å / SU ML: 0.0802 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 14.7979
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→32.88 Å
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Refine LS restraints |
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LS refinement shell |
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