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Yorodumi- PDB-2b3b: Thermus thermophilus Glucose/Galactose Binding Protein With Bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b3b | ||||||
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Title | Thermus thermophilus Glucose/Galactose Binding Protein With Bound Glucose | ||||||
Components | glucose-binding protein | ||||||
Keywords | SUGAR BINDING PROTEIN / protein-carbohydrate complex / glucose / galactose / periplasmic binding protein | ||||||
Function / homology | Function and homology information : / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Thermus thermophilus HB27 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Cuneo, M.J. / Changela, A. / Warren, J.J. / Beese, L.S. / Hellinga, H.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: The crystal structure of a thermophilic glucose binding protein reveals adaptations that interconvert mono and di-saccharide binding sites. Authors: Cuneo, M.J. / Changela, A. / Warren, J.J. / Beese, L.S. / Hellinga, H.W. | ||||||
History |
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Remark 999 | SEQEUNCE THE AUTHORS STATE THAT THE DISCREPANCIES BETWEEN GENBANK AND AMINO ACID SEQUENCE IN PDB ...SEQEUNCE THE AUTHORS STATE THAT THE DISCREPANCIES BETWEEN GENBANK AND AMINO ACID SEQUENCE IN PDB ARE DUE TO ERRORS IN THE PUBLISHED SEQUENCE OR ERRORS AS A RESULT OF CLONING THE GENE FOR CRYSTALLIZATION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b3b.cif.gz | 489.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b3b.ent.gz | 401.2 KB | Display | PDB format |
PDBx/mmJSON format | 2b3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b3b_validation.pdf.gz | 501 KB | Display | wwPDB validaton report |
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Full document | 2b3b_full_validation.pdf.gz | 511.3 KB | Display | |
Data in XML | 2b3b_validation.xml.gz | 98.4 KB | Display | |
Data in CIF | 2b3b_validation.cif.gz | 144.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/2b3b ftp://data.pdbj.org/pub/pdb/validation_reports/b3/2b3b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 44091.215 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Species: Thermus thermophilus / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: ttc0328 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Rosetta Gami / References: UniProt: Q72KX2 #2: Sugar | ChemComp-GLC / #3: Sugar | #4: 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: 2.6 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 10% (w/v) Isopropanol, 0.1M Sodium Citrate pH5.6, 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97917 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 181610 / % possible obs: 95.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.086 / Χ2: 1.767 |
Reflection shell | Resolution: 1.95→2.02 Å / % possible obs: 82.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.4 / Num. measured obs: 15463 / Χ2: 0.818 / % possible all: 82.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.81 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2.4 / ESU R: 0.175 / ESU R Free: 0.155 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.086 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.953→2.004 Å / Total num. of bins used: 20
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