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Yorodumi- PDB-3csb: Crystal Structure of Monobody YSX1/Maltose Binding Protein Fusion... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3csb | ||||||
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Title | Crystal Structure of Monobody YSX1/Maltose Binding Protein Fusion Complex | ||||||
Components | Maltose-binding protein Monobody YSX1 Fusion | ||||||
Keywords | DE NOVO PROTEIN / SUGAR BINDING PROTEIN / Engineered Binding Protein / Antibody Mimic / Synthetic Protein Interface / Minimalist Protein Interface | ||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å | ||||||
Authors | Gilbreth, R.N. / Koide, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: A Dominant Conformational Role for Amino Acid Diversity in Minimalist Protein-Protein Interfaces Authors: Gilbreth, R.N. / Esaki, K. / Koide, A. / Sidhu, S.S. / Koide, S. #1: 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 | 3csb.cif.gz | 112.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3csb.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 3csb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3csb_validation.pdf.gz | 476.6 KB | Display | wwPDB validaton report |
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Full document | 3csb_full_validation.pdf.gz | 487.3 KB | Display | |
Data in XML | 3csb_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 3csb_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/3csb ftp://data.pdbj.org/pub/pdb/validation_reports/cs/3csb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50779.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: malE includes residues 5-370, Monobody YSX1 377-467, 371-373 comprise an engineered linker Source: (gene. exp.) Escherichia coli, synthetic / Gene: malE / Plasmid: pHFT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9 |
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-Non-polymers , 7 types, 226 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | #4: Chemical | ChemComp-PGE / | #5: Chemical | ChemComp-PG4 / | #6: Chemical | ChemComp-1PE / | #7: Chemical | ChemComp-PEG / #8: 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: 3.24 Å3/Da / Density % sol: 61.99 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 41% polyethelyeneglycol-400, 2% 2-methyl-2,4-pentanediol, 50 mM MnCl2, 0.1 M 2-(N-morpholino)ethanesulfonic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 21, 2007 |
Radiation | Monochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.999→50 Å / Num. all: 45823 / Num. obs: 45823 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.999→2.07 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.123 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 37.551 Å2
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Refinement step | Cycle: LAST / Resolution: 1.999→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.999→2.051 Å / Total num. of bins used: 20
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