+Open data
-Basic information
Entry | Database: PDB / ID: 3a8e | |||||||||
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Title | The structure of AxCesD octamer complexed with cellopentaose | |||||||||
Components | Cellulose synthase operon protein D | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / COMPLEX / OCTAMER / TETRAMER OF DIMERS / MOLECULE RING / CELLULOSE BIOSYNTHESIS / BCSD / TC | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Acetobacter xylinus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å | |||||||||
Authors | Hu, S.Q. / Tajima, K. / Zhou, Y. / Yao, M. / Tanaka, I. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structure of bacterial cellulose synthase subunit D octamer with four inner passageways Authors: Hu, S.Q. / Gao, Y.G. / Tajima, K. / Sunagawa, N. / Zhou, Y. / Kawano, S. / Fujiwara, T. / Yoda, T. / Shimura, D. / Satoh, Y. / Munekata, M. / Tanaka, I. / Yao, M. #1: Journal: Protein Pept.Lett. / Year: 2008 Title: Purification, crystallization and preliminary X-ray studies of AxCesD required for efficient cellulose biosynthesis in Acetobacter xylinum Authors: Yao, M. / Hu, S.Q. / Gao, Y.G. / Tajima, K. / Yoda, T. / Shimura, D. / Satoh, Y. / Kawano, S. / Tanaka, I. / Munekata, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a8e.cif.gz | 256 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a8e.ent.gz | 212.8 KB | Display | PDB format |
PDBx/mmJSON format | 3a8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a8e_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3a8e_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3a8e_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 3a8e_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/3a8e ftp://data.pdbj.org/pub/pdb/validation_reports/a8/3a8e | HTTPS FTP |
-Related structure data
Related structure data | 3aj1C 3aj2C 2z9f C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18217.715 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetobacter xylinus (bacteria) / Strain: ATCC 23769 / Gene: acsD / Plasmid: PET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P37719 #2: Polysaccharide | #3: 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: 3.28 Å3/Da / Density % sol: 62.51 % / Mosaicity: 0.392 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.1M PHOSPHATE-CITRATE, 0.2M LI2SO4, 10% (V/V) ISO-PROPANOL, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2007 / 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: 3→50 Å / Num. obs: 19771 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 70.456 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Χ2: 1.017 / Net I/σ(I): 24.067 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 9 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.41 / Num. unique all: 1944 / Rsym value: 0.399 / Χ2: 0.697 / % possible all: 99.9 |
-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 2Z9F 2z9f Resolution: 3→19.94 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 35.882 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; LAFIRE was also used in refinement
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.634 Å2
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Refinement step | Cycle: LAST / Resolution: 3→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.002→3.079 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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