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Yorodumi- PDB-1dmb: REFINED 1.8 ANGSTROMS STRUCTURE REVEALS THE MECHANISM OF BINDING ... -
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-Basic information
Entry | Database: PDB / ID: 1dmb | |||||||||
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Title | REFINED 1.8 ANGSTROMS STRUCTURE REVEALS THE MECHANISM OF BINDING OF A CYCLIC SUGAR, BETA-CYCLODEXTRIN, TO THE MALTODEXTRIN BINDING PROTEIN | |||||||||
Components | D-MALTODEXTRIN BINDING PROTEIN | |||||||||
Keywords | SUGAR TRANSPORT | |||||||||
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) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | |||||||||
Authors | Sharff, A.J. / Quiocho, F.A. | |||||||||
Citation | Journal: Biochemistry / Year: 1993 Title: Refined 1.8-A structure reveals the mode of binding of beta-cyclodextrin to the maltodextrin binding protein. Authors: Sharff, A.J. / Rodseth, L.E. / Quiocho, F.A. #1: Journal: Biochemistry / Year: 1992 Title: Crystallographic Evidence of a Large Ligand-Induced Hinge-Twist Motion between the Two Domains of the Maltodextrin Binding Protein Involved in Active Transport and Chemotaxis Authors: Sharff, A.J. / Rodseth, L.E. / Spurlino, J.C. / Quiocho, F.A. #2: Journal: J.Biol.Chem. / Year: 1991 Title: The 2.3 Angstroms Resolution Structure of the Maltose-or Maltodextrin-Binding Protein, a Primary Receptor of Bacterial Active Transport and Chemotaxis Authors: Spurlino, J.C. / Lu, G.-Y. / Quiocho, F.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dmb.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dmb.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 1dmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dmb_validation.pdf.gz | 976 KB | Display | wwPDB validaton report |
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Full document | 1dmb_full_validation.pdf.gz | 991.4 KB | Display | |
Data in XML | 1dmb_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 1dmb_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/1dmb ftp://data.pdbj.org/pub/pdb/validation_reports/dm/1dmb | HTTPS FTP |
-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: 40753.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P02928, UniProt: P0AEX9*PLUS |
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#2: Polysaccharide | Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.64 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.2 / Method: vapor diffusion, hanging drop / Details: used to seed | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.73 Å / Num. obs: 32945 / % possible obs: 87 % / Num. measured all: 63892 / Rmerge(I) obs: 0.0296 |
-Processing
Software |
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Refinement | Resolution: 1.8→10 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. reflection obs: 30840 / σ(I): 2 / Rfactor obs: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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