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Yorodumi- PDB-4i86: Crystal structure of PilZ domain of CeSA from cellulose synthesiz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i86 | ||||||
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Title | Crystal structure of PilZ domain of CeSA from cellulose synthesizing bacterium | ||||||
Components | Cellulose synthase 1 | ||||||
Keywords | TRANSFERASE / beta-barrel fold / c-di-GMP Binding | ||||||
Function / homology | Function and homology information cellulose synthase (UDP-forming) / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / UDP-glucose metabolic process / cyclic-di-GMP binding / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Gluconacetobacter xylinus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å | ||||||
Authors | Fujiwara, T. / Komoda, K. / Sakurai, N. / Tanaka, I. / Yao, M. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2013 Title: The c-di-GMP recognition mechanism of the PilZ domain of bacterial cellulose synthase subunit A Authors: Fujiwara, T. / Komoda, K. / Sakurai, N. / Tajima, K. / Tanaka, I. / Yao, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i86.cif.gz | 50.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i86.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 4i86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/4i86 ftp://data.pdbj.org/pub/pdb/validation_reports/i8/4i86 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12295.118 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, UNP residues 572-670 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gluconacetobacter xylinus (bacteria) / Gene: acsAB / Plasmid: pET26B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0CW87, cellulose synthase (UDP-forming) #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: 1.86 Å3/Da / Density % sol: 33.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 0.1M phosphate-citrate, 30%(v/v) PEG300, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 5, 2011 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.098→45 Å / Num. obs: 11236 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 24.52 |
Reflection shell | Resolution: 2.1→2.22 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1767 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.098→35.153 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8042 / SU ML: 0.47 / σ(F): 2.01 / Phase error: 25.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.971 Å2 / ksol: 0.412 e/Å3 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.9 Å2 / Biso mean: 33.8746 Å2 / Biso min: 14.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.098→35.153 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: 4 / % reflection obs: 100 %
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