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- PDB-4zxl: CpOGA D298N in complex with Drosophila HCF -derived Thr-O-GlcNAc ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zxl | ||||||
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Title | CpOGA D298N in complex with Drosophila HCF -derived Thr-O-GlcNAc peptide | ||||||
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![]() | HYDROLASE/PEPTIDE / HYDROLASE-O-GlcNAcylated PEPTIDE complex TIM BARREL Thr-O-GlcNAc / HYDROLASE-PEPTIDE complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Selvan, N. / van Aalten, D.M.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A mutant O-GlcNAcase as a probe to reveal global dynamics of protein O-GlcNAcylation during Drosophila embryonic development. Authors: Mariappa, D. / Selvan, N. / Borodkin, V.S. / Alonso, J. / Ferenbach, A.T. / Shepherd, C. / Navratilova, I.H. / van Aalten, D.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 250.7 KB | Display | ![]() |
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PDB format | ![]() | 199.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.2 KB | Display | ![]() |
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Full document | ![]() | 450.7 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 30.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ydsS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 374.389 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Thr-O-GlcNAc containing peptide from drosophila HCF Source: (synth.) ![]() ![]() | ||
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#2: Protein | Mass: 65099.934 Da / Num. of mol.: 1 / Fragment: UNP residues 39-617 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: nagJ, CPF_1442 / Production host: ![]() ![]() References: UniProt: Q0TR53, protein O-GlcNAcase, beta-N-acetylhexosaminidase | ||
#3: Sugar | ChemComp-NAG / | ||
#4: Chemical | ChemComp-CD / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.6 Å3/Da / Density % sol: 73.26 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: CpOGA D298N was concentrated to 35 mg/ml in 25 mM Tris/HCl (pH 8.0) and crystallized from 0.175 M CdSO4 and 0.6 M sodium acetate pH 7.5 PH range: 6.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→34.9 Å / Num. obs: 36087 / % possible obs: 99.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.862 / Num. unique all: 4368 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2yds Resolution: 2.6→34.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 19.513 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 42.751 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→34.9 Å
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Refine LS restraints |
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