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Yorodumi- PDB-3vxb: Crystal Structure of BxlE from Streptomyces thermoviolaceus OPC-520 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vxb | ||||||
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Title | Crystal Structure of BxlE from Streptomyces thermoviolaceus OPC-520 | ||||||
Components | Putative sugar-binding lipoprotein | ||||||
Keywords | SUGAR BINDING PROTEIN / ABC Transporter | ||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta / Putative sugar-binding lipoprotein Function and homology information | ||||||
Biological species | Streptomyces thermoviolaceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Tomoo, K. / Ishida, T. / Miyamoto, K. / Tsujibo, H. | ||||||
Citation | Journal: To be published Title: Crystal Structure of Xylooligosaccharide-Binding Protein from Streptomyces thermoviolaceus OPC-520: Dramatic Conformational Change with Ligand binding Authors: Tomoo, K. / Ishida, T. / Miyamoto, K. / Tsujibo, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vxb.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vxb.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 3vxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/3vxb ftp://data.pdbj.org/pub/pdb/validation_reports/vx/3vxb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46707.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces thermoviolaceus (bacteria) Gene: bxlD / Production host: Escherichia coli (E. coli) / References: UniProt: Q76BU9 | ||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.2 Details: 25% PEG 3350, 0.1M citrate, pH 3.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE | |||||||||||||||
Radiation |
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.65→34.2 Å / Num. all: 43438 / Num. obs: 39659 / % possible obs: 91.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.026 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→29.31 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.366 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.158 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.313 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→29.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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