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Yorodumi- PDB-3bcv: Crystal structure of a putative glycosyltransferase from Bacteroi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bcv | ||||||
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Title | Crystal structure of a putative glycosyltransferase from Bacteroides fragilis | ||||||
Components | Putative glycosyltransferase protein | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Bacteroides fragilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å | ||||||
Authors | Palani, K. / Kumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bcv.cif.gz | 87.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bcv.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/3bcv ftp://data.pdbj.org/pub/pdb/validation_reports/bc/3bcv | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF2801 / Plasmid: BC-pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5LBM4 #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: 2.7 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: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.35→27.83 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 59750.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber 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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