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Yorodumi- PDB-3dec: Crystal structure of a glycosyl hydrolases family 2 protein from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dec | ||||||
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Title | Crystal structure of a glycosyl hydrolases family 2 protein from Bacteroides thetaiotaomicron | ||||||
Components | Beta-galactosidase | ||||||
Keywords | HYDROLASE / Glucosyl Hydrolase Family 2 / BETA-GALACTOSIDASE / NYSGXRC / PROTEIN STRUCTURE INITIATIVE II (PSI-II) / JELLY-ROLL FOLD / IMMUNOGLOBULIN-LIKE FOLD / TIM-BARREL DOMAIN / STRUCTURAL GENOMICS / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kumaran, D. / Bonanno, J. / Romero, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of a Glycosyl Hydrolases Family 2 protein from Bacteroides thetaiotaomicron. Authors: Kumaran, D. / Bonanno, J. / Romero, R. / 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 | 3dec.cif.gz | 210 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dec.ent.gz | 166 KB | Display | PDB format |
PDBx/mmJSON format | 3dec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/3dec ftp://data.pdbj.org/pub/pdb/validation_reports/de/3dec | HTTPS FTP |
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-Related structure data
Related structure data | 3bgaS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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: 114830.828 Da / Num. of mol.: 1 / Fragment: Residues 29-1024 / Mutation: A538V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Strain: VPI-5482 / DSM 2079 / NCTC 10582 / E50 / Gene: BT_3179 / Plasmid: pSGX4(BS) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A2X6 |
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#2: Chemical | ChemComp-K / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 50% PEG MME 2000, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 11, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47 Å / Num. all: 29182 / Num. obs: 29182 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 5.4 / Num. unique all: 3846 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3BGA Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.868 / SU B: 13.441 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 | 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: 30.746 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.871 Å / Total num. of bins used: 20
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