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- PDB-3bcv: Crystal structure of a putative glycosyltransferase from Bacteroi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bcv | ||||||
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Title | Crystal structure of a putative glycosyltransferase from Bacteroides fragilis | ||||||
![]() | Putative glycosyltransferase protein | ||||||
![]() | TRANSFERASE / Glycosyltransferase / Protein Structure Initiative II / PSI-II / 12059a / NYSGXRC / Structural Genomics / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Glycosyltransferase 2-like / Glycosyl transferase family 2 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / transferase activity / Alpha-Beta Complex / Alpha Beta / Putative glycosyltransferase protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Palani, K. / Kumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Crystal structure of a putative glycosyltransferase from Bacteroides fragilis. Authors: Palani, K. / Kumaran, D. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.5 KB | Display | ![]() |
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PDB format | ![]() | 71.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.7 KB | Display | ![]() |
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Full document | ![]() | 443.2 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27544.617 Da / Num. of mol.: 2 / Fragment: Residues 2-230 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: 2.7 Å3/Da / Density % sol: 54.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M Sodium acetate trihydrate, 0.2M Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2007 / Details: Mirrors |
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 23202 / Num. obs: 23202 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.6 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2 / Num. unique all: 2056 / % possible all: 84.6 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.0043 Å2 / ksol: 0.345065 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→27.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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