+Open data
-Basic information
Entry | Database: PDB / ID: 3pms | ||||||
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Title | Recombinant peptide: N-glycanase F (PNGase F) | ||||||
Components | Peptide:N-glycosidase F | ||||||
Keywords | HYDROLASE / Jelly Roll Fold / N-Glycanase | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / hydrolase activity, acting on glycosyl bonds Similarity search - Function | ||||||
Biological species | Elizabethkingia meningoseptica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å | ||||||
Authors | Filitcheva, J. / Anderson, B.F. / Norris, G.E. | ||||||
Citation | Journal: To be Published Title: Recombinant peptide:N-glycanase F (PNGase F) Authors: Filitcheva, J. / Anderson, B.F. / Norris, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pms.cif.gz | 90.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pms.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/3pms ftp://data.pdbj.org/pub/pdb/validation_reports/pm/3pms | HTTPS FTP |
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-Related structure data
Related structure data | 1pgsS 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: 36292.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria) Strain: CDC 3552 / Gene: png / Plasmid: OPH6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9XBM8, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #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: 2.31 Å3/Da / Density % sol: 46.7 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 25% PEG 4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 10, 2009 |
Radiation | Monochromator: Capillary optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→40.41 Å / Num. all: 43449 / Num. obs: 41972 / % possible obs: 96.6 % / Rmerge(I) obs: 0.057 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PGS Resolution: 1.57→34.02 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.281 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.05 Å2 / Biso mean: 18.3064 Å2 / Biso min: 6.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→34.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.57→1.611 Å / Total num. of bins used: 20
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