+Open data
-Basic information
Entry | Database: PDB / ID: 6rhe | |||||||||
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Title | CpOGA D298N in complex with hOGA-derived S-GlcNAc peptide | |||||||||
Components |
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Keywords | HYDROLASE / N-Acetyl Glucosamine | |||||||||
Function / homology | Function and homology information protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Clostridium perfringens ATCC 13124 (bacteria) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||
Authors | Van Aalten, D. / Bartual, S.G. / Gorelik, A. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2019 Title: Genetic recoding to dissect the roles of site-specific protein O-GlcNAcylation. Authors: Gorelik, A. / Bartual, S.G. / Borodkin, V.S. / Varghese, J. / Ferenbach, A.T. / van Aalten, D.M.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rhe.cif.gz | 134.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rhe.ent.gz | 101.4 KB | Display | PDB format |
PDBx/mmJSON format | 6rhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rhe_validation.pdf.gz | 460 KB | Display | wwPDB validaton report |
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Full document | 6rhe_full_validation.pdf.gz | 464.5 KB | Display | |
Data in XML | 6rhe_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 6rhe_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/6rhe ftp://data.pdbj.org/pub/pdb/validation_reports/rh/6rhe | HTTPS FTP |
-Related structure data
Related structure data | 2ydqS 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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Unit cell |
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-Components
#1: Protein | Mass: 66348.258 Da / Num. of mol.: 1 / Mutation: D298N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens ATCC 13124 (bacteria) Strain: ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A Gene: nagJ, CPF_1442 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q0TR53, protein O-GlcNAcase | ||||
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#2: Protein/peptide | Mass: 411.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
#3: Chemical | ChemComp-CD / #4: Sugar | ChemComp-NAG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.52 Å3/Da / Density % sol: 72.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1:1 drops of proytein mixed with crystallisation buffer: 0.175 M CdSO4 and 0.6 M NaAc |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→48.17 Å / Num. obs: 19800 / % possible obs: 94.1 % / Redundancy: 3.2 % / Rpim(I) all: 0.09 / Net I/σ(I): 8 |
Reflection shell | Resolution: 3.1→3.31 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3629 / Rpim(I) all: 0.72 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YDQ Resolution: 3.1→48.17 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 17.396 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 5.964 / ESU R Free: 0.375 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.536 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→48.17 Å
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Refine LS restraints |
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