+Open data
-Basic information
Entry | Database: PDB / ID: 4r4x | ||||||
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Title | Structure of PNGF-II in C2 space group | ||||||
Components | PNGF-II | ||||||
Keywords | HYDROLASE / N-glycanase (PNGase) / PNGase F / Deglycosylation / N-glycoproteins | ||||||
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 / metal ion binding Similarity search - Function | ||||||
Biological species | Elizabethkingia meningoseptica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sun, G. / Yu, X. / Celimuge / Wang, L. / Li, M. / Gan, J. / Qu, D. / Ma, J. / Chen, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Identification and Characterization of a Novel Prokaryotic Peptide: N-glycosidase from Elizabethkingia meningoseptica Authors: Sun, G. / Yu, X. / Celimuge / Wang, L. / Li, M. / Gan, J. / Qu, D. / Ma, J. / Chen, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r4x.cif.gz | 130.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r4x.ent.gz | 100.1 KB | Display | PDB format |
PDBx/mmJSON format | 4r4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r4x_validation.pdf.gz | 428.1 KB | Display | wwPDB validaton report |
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Full document | 4r4x_full_validation.pdf.gz | 432.5 KB | Display | |
Data in XML | 4r4x_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 4r4x_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/4r4x ftp://data.pdbj.org/pub/pdb/validation_reports/r4/4r4x | HTTPS FTP |
-Related structure data
Related structure data | 4r4zC 3ks7S 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
#1: Protein | Mass: 61527.168 Da / Num. of mol.: 1 / Fragment: PNGF-II Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria) Strain: FMS-007 / Gene: CP006576 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 References: UniProt: A0A090KI56*PLUS, DNA-directed DNA polymerase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.35 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG4000, 0.01M MgCl2, 0.2M KCl, 0.05M sodium cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 196 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2013 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 48606 / Num. obs: 47585 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.02 / Num. unique all: 4804 / Rsym value: 0.424 / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS7 Resolution: 1.9→29.97 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.634 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS
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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: 20.085 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.97 Å
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Refine LS restraints |
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