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Yorodumi- PDB-5mi6: BtGH84 mutant with covalent modification by MA3 in complex with T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mi6 | ||||||
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Title | BtGH84 mutant with covalent modification by MA3 in complex with Thiamet G | ||||||
Components | O-GlcNAcase BT_4395 | ||||||
Keywords | HYDROLASE / activator | ||||||
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 / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / identical protein binding Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Darby, J.F. / Davies, G.J. / Hubbard, R.E. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Chem Sci / Year: 2017 Title: Increase of enzyme activity through specific covalent modification with fragments. Authors: Darby, J.F. / Atobe, M. / Firth, J.D. / Bond, P. / Davies, G.J. / O'Brien, P. / Hubbard, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mi6.cif.gz | 165 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mi6.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mi6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mi6_validation.pdf.gz | 478.8 KB | Display | wwPDB validaton report |
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Full document | 5mi6_full_validation.pdf.gz | 482.4 KB | Display | |
Data in XML | 5mi6_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 5mi6_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/5mi6 ftp://data.pdbj.org/pub/pdb/validation_reports/mi/5mi6 | HTTPS FTP |
-Related structure data
Related structure data | 5mi4C 5mi5C 5mi7C 2choS 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 83601.453 Da / Num. of mol.: 1 / Mutation: C420S, Y550C, C654S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Gene: BT_4395 / Plasmid: YSBLLICPET28 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: Q89ZI2, protein O-GlcNAcase, beta-N-acetylhexosaminidase |
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-Non-polymers , 5 types, 331 molecules
#2: Chemical | ChemComp-NHT / ( | ||||
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#3: Chemical | ChemComp-7NQ / ~{ | ||||
#4: Chemical | #5: Chemical | ChemComp-CA / | #6: 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: 3.12 Å3/Da / Density % sol: 60.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 4% PEG 8K, 125mM Imidazole, 3% TMAO, 15% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 1, 2016 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→49.66 Å / Num. obs: 70077 / % possible obs: 99.5 % / Redundancy: 3.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.112 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2→2.16 Å / Redundancy: 3 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.2 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CHO Resolution: 2→49.66 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.689 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.147 / 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: 36.712 Å2
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Refinement step | Cycle: 1 / Resolution: 2→49.66 Å
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Refine LS restraints |
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