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Yorodumi- PDB-2obg: Crystal Structure of Monobody MBP-74/Maltose Binding Protein Fusi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2obg | ||||||
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Title | Crystal Structure of Monobody MBP-74/Maltose Binding Protein Fusion Complex | ||||||
Components | Maltose Binding periplasmic Protein and Monobody MBP-74 Fusion protein | ||||||
Keywords | DE NOVO PROTEIN / PROTEIN BINDING / Domain swapping / Binding Protein / Antibody Mimic / Binary Interface | ||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Gilbreth, R.N. / Tereshko, V. / Koide, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: High-affinity single-domain binding proteins with a binary-code interface. Authors: Koide, A. / Gilbreth, R.N. / Esaki, K. / Tereshko, V. / Koide, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2obg.cif.gz | 99.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2obg.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 2obg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/2obg ftp://data.pdbj.org/pub/pdb/validation_reports/ob/2obg | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50543.738 Da / Num. of mol.: 1 / Fragment: MBP (residues 5-370), MBP-74 (residues 1001-1093) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli, synthetic construct / Genus: Escherichia, / Species: , / Strain: , / Gene: malE / Plasmid: pHFT2-MBP/MBP-74 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9 |
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#2: 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: 2.61 Å3/Da / Density % sol: 52.86 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG-1000, 0.1 M Na/K phosphate, 0.2 M NaCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 21507 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 17.416 / SU ML: 0.207 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.262 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.11 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.41 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 90.5181 Å / Origin y: 62.1247 Å / Origin z: 26.245 Å
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