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Yorodumi- PDB-5vvt: Structural Investigations of the Substrate Specificity of Human O... -
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-Basic information
Entry | Database: PDB / ID: 5vvt | ||||||
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Title | Structural Investigations of the Substrate Specificity of Human O-GlcNAcase | ||||||
Components |
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Keywords | HYDROLASE / OGA / Human O-GlcNAcase / ELK1 | ||||||
Function / homology | Function and homology information hippocampal neuron apoptotic process / hyalurononglucosaminidase activity / glycoprotein metabolic process / N-acetylglucosamine metabolic process / glycoprotein catabolic process / protein O-GlcNAcase / : / : / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / response to fibroblast growth factor ...hippocampal neuron apoptotic process / hyalurononglucosaminidase activity / glycoprotein metabolic process / N-acetylglucosamine metabolic process / glycoprotein catabolic process / protein O-GlcNAcase / : / : / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / response to fibroblast growth factor / cellular response to testosterone stimulus / protein O-linked glycosylation / NGF-stimulated transcription / protein deglycosylation / ERK/MAPK targets / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / response to light stimulus / axon terminus / nuclear receptor coactivator activity / liver development / mitochondrial membrane / beta-N-acetylglucosaminidase activity / lung development / cellular response to gamma radiation / HCMV Early Events / sequence-specific double-stranded DNA binding / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / neuronal cell body / chromatin binding / dendrite / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Li, B. / Jiang, J. / Li, H. / Hu, C.-W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Structural insights into the substrate binding adaptability and specificity of human O-GlcNAcase. Authors: Li, B. / Li, H. / Hu, C.W. / Jiang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vvt.cif.gz | 189.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vvt.ent.gz | 147.1 KB | Display | PDB format |
PDBx/mmJSON format | 5vvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vvt_validation.pdf.gz | 480.6 KB | Display | wwPDB validaton report |
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Full document | 5vvt_full_validation.pdf.gz | 496.7 KB | Display | |
Data in XML | 5vvt_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 5vvt_validation.cif.gz | 44.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/5vvt ftp://data.pdbj.org/pub/pdb/validation_reports/vv/5vvt | HTTPS FTP |
-Related structure data
Related structure data | 5vvoC 5vvuC 5vvvC 5vvxC 5un8S C: citing same article (ref.) 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 59 - 694 / Label seq-ID: 1 - 494
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-Components
#1: Protein | Mass: 57822.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MGEA5, HEXC, KIAA0679, MEA5 / Production host: Escherichia coli (E. coli) References: UniProt: O60502, protein O-GlcNAcase, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Protein/peptide | Mass: 950.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P19419*PLUS #3: Sugar | #4: 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: 2.72 Å3/Da / Density % sol: 54.75 % |
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Crystal grow | Temperature: 293 K / Method: evaporation Details: 0.024 M ammonium citrate tribasic (pH 7.0), 0.015 M MES monohydrate, 0.096 M potassium thiocyanate, 0.25 M Sodium acetate trihydrate, 0.037 M imidazole, 0.002 M zinc sulfate heptahydrate, 9. ...Details: 0.024 M ammonium citrate tribasic (pH 7.0), 0.015 M MES monohydrate, 0.096 M potassium thiocyanate, 0.25 M Sodium acetate trihydrate, 0.037 M imidazole, 0.002 M zinc sulfate heptahydrate, 9.6 % w/v polyethylene glycol 3,350, 2.4 % w/v polyethylene glycol monomethyl ether 2,000, and 4% w/v polyethylene glycol monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 31, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 31269 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rpim(I) all: 0.046 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.8→2.85 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1582 / CC1/2: 0.73 / Rpim(I) all: 0.4 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UN8 Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.886 / SU B: 19.497 / SU ML: 0.368 / Cross valid method: THROUGHOUT / ESU R: 1.262 / ESU R Free: 0.403
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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: 70.712 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→50 Å
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