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- PDB-3aj2: The structure of AxCeSD octamer (C-terminal HIS-tag) from Acetoba... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3aj2 | |||||||||
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Title | The structure of AxCeSD octamer (C-terminal HIS-tag) from Acetobacter xylinum | |||||||||
![]() | Cellulose synthase operon protein D | |||||||||
![]() | BIOSYNTHETIC PROTEIN / ALPHA AND BETA FOLD / OCTAMER / TETRAMER OF DIMERS / MOLECULE RING / CELLULOSE BIOSYNTHESIS / STRUCTURAL GENOMICS / NPPSFA / NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Hu, S.Q. / Tajima, K. / Zhou, Y. / Tanaka, I. / Yao, M. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 243.3 KB | Display | ![]() |
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PDB format | ![]() | 201 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.5 KB | Display | ![]() |
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Full document | ![]() | 493.3 KB | Display | |
Data in XML | ![]() | 29.6 KB | Display | |
Data in CIF | ![]() | 41.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a8eC ![]() 3aj1C ![]() 2z9e C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.96 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 5.4 Details: 0.2M LI2SO4, 0.1M PHOSPHATE-CITRATE pH 5.4, 10% (V/V) ISO-PROPANOL, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 26, 2007 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 27157 / Num. obs: 27157 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 65.2 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.432 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Z9E ![]() 2z9e Resolution: 2.7→19.8 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / SU B: 22.737 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.637 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 64.396 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.701→2.77 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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