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Yorodumi- PDB-2f4o: The Mouse PNGase-HR23 Complex Reveals a Complete Remodulation of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f4o | ||||||
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Title | The Mouse PNGase-HR23 Complex Reveals a Complete Remodulation of the Protein-Protein Interface Compared to its Yeast Orthologs | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / GLYCOPROTEINS / UBIQUITIN-DEPENDENT PROTEIN DEGRADATION / NUCLEOTIDE EXCISION REPAIR / PEPTIDE:N-GLYCANASE / TRANSGLUTAMINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / DNA Damage Recognition in GG-NER / XPC complex / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / glycoprotein catabolic process / DNA damage sensor activity / regulation of proteasomal ubiquitin-dependent protein catabolic process ...peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / DNA Damage Recognition in GG-NER / XPC complex / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / glycoprotein catabolic process / DNA damage sensor activity / regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to interleukin-7 / proteasome binding / protein quality control for misfolded or incompletely synthesized proteins / polyubiquitin modification-dependent protein binding / embryonic organ development / proteasome complex / ubiquitin binding / nucleotide-excision repair / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / collagen-containing extracellular matrix / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA damage response / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Zhao, G. / Zhou, X. / Wang, L. / Kisker, C. / Lennarz, W.J. / Schindelin, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structure of the mouse peptide N-glycanase-HR23 complex suggests co-evolution of the endoplasmic reticulum-associated degradation and DNA repair pathways. Authors: Zhao, G. / Zhou, X. / Wang, L. / Li, G. / Kisker, C. / Lennarz, W.J. / Schindelin, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f4o.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f4o.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 2f4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f4o_validation.pdf.gz | 445 KB | Display | wwPDB validaton report |
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Full document | 2f4o_full_validation.pdf.gz | 456 KB | Display | |
Data in XML | 2f4o_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 2f4o_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/2f4o ftp://data.pdbj.org/pub/pdb/validation_reports/f4/2f4o | HTTPS FTP |
-Related structure data
Related structure data | 2f4mSC 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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2 |
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Unit cell |
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Details | Heterodimer covalently modified by inhibitor. |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 34866.730 Da / Num. of mol.: 1 / Fragment: Catalytic domain, residues 164-450 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL References: GenBank: 30517852, UniProt: Q9JI78*PLUS, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase |
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#2: Protein | Mass: 7185.165 Da / Num. of mol.: 1 / Fragment: XPCB domain, residues 273-332 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rad23b, Mhr23b / Plasmid: pTYb1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: P54728 |
-Protein/peptide , 1 types, 1 molecules I
#3: Protein/peptide | |
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-Non-polymers , 3 types, 21 molecules
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: 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: 2.23 Å3/Da / Density % sol: 44.89 % |
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Crystal grow | Temperature: 291 K / pH: 8.5 Details: 0.1 M Tris-HCl, 28-32% PEG4000, 0.2 M sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 10, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 17174 / Num. obs: 17174 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.098 / Rsym value: 0.055 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.216 / % possible all: 49.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2F4M Resolution: 2.26→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.898 / SU B: 23.605 / SU ML: 0.274 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.665 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 62.44 Å2
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Refinement step | Cycle: LAST / Resolution: 2.26→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.26→2.32 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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