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Yorodumi- PDB-4knc: Structural and functional characterization of Pseudomonas aerugin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4knc | ||||||
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Title | Structural and functional characterization of Pseudomonas aeruginosa AlgX | ||||||
Components | Alginate biosynthesis protein AlgX | ||||||
Keywords | SUGAR BINDING PROTEIN / alginate acetylation / SGNH hydrolase / carbohydrate-binding domain | ||||||
Function / homology | Function and homology information alginic acid biosynthetic process / single-species biofilm formation / acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / periplasmic space Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.141 Å | ||||||
Authors | Riley, L.M. / Weadge, J.T. / Baker, P. / Robinson, H. / Codee, J.D.C. / Tipton, P.A. / Ohman, D.E. / Howell, P.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural and Functional Characterization of Pseudomonas aeruginosa AlgX: ROLE OF AlgX IN ALGINATE ACETYLATION. Authors: Riley, L.M. / Weadge, J.T. / Baker, P. / Robinson, H. / Codee, J.D. / Tipton, P.A. / Ohman, D.E. / Howell, P.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4knc.cif.gz | 345.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4knc.ent.gz | 290.8 KB | Display | PDB format |
PDBx/mmJSON format | 4knc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/4knc ftp://data.pdbj.org/pub/pdb/validation_reports/kn/4knc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 51011.910 Da / Num. of mol.: 2 / Fragment: UNP residues 27-474 Source method: isolated from a genetically manipulated source Details: codon-optimized synthetic algX gene prepared by GenScript Corporation, for expression in E. coli. Based on wild-type algX from P. aeruginosa PAO1 Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: algX, PA3546 / Plasmid: pET-24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RP / References: UniProt: Q51372 #2: 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: 2.32 Å3/Da / Density % sol: 46.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: 25% PEG3000, 100 mM sodium citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.141→50 Å / Num. obs: 52346 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Rmerge(I) obs: 0.081 / Χ2: 1.802 / Net I/σ(I): 10.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.141→43.643 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7982 / SU ML: 0.24 / σ(F): 0 / Phase error: 26.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.09 Å2 / Biso mean: 50.108 Å2 / Biso min: 23.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.141→43.643 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 143.8896 Å / Origin y: 15.1334 Å / Origin z: 38.1586 Å
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Refinement TLS group |
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