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Yorodumi- PDB-2dri: PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dri | |||||||||
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Title | PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS | |||||||||
Components | D-RIBOSE-BINDING PROTEIN | |||||||||
Keywords | SUGAR TRANSPORT | |||||||||
Function / homology | Function and homology information D-ribose transmembrane transport / monosaccharide binding / positive chemotaxis / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.6 Å | |||||||||
Authors | Mowbray, S.L. / Cole, L.B. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1994 Title: Probing protein-protein interactions. The ribose-binding protein in bacterial transport and chemotaxis. Authors: Bjorkman, A.J. / Binnie, R.A. / Zhang, H. / Cole, L.B. / Hermodson, M.A. / Mowbray, S.L. #1: Journal: J.Mol.Biol. / Year: 1992 Title: 1.7 Angstroms X-Ray Structure of the Periplasmic Ribose Receptor from Escherichia Coli Authors: Mowbray, S.L. / Cole, L.B. #2: Journal: Protein Sci. / Year: 1992 Title: Functional Mapping of the Surface of Escherichia Coli Ribose-Binding Protein: Mutations which Affect Chemotaxis and Transport Authors: Binnie, R.A. / Zhang, H. / Mowbray, S. / Hermodson, M.A. #3: Journal: J.Mol.Biol. / Year: 1990 Title: Preliminary X-Ray Data for the Periplasmic Ribose Receptor from Escherichia Coli Authors: Mahendroo, M. / Cole, L.B. / Mowbray, S.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dri.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dri.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 2dri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dri_validation.pdf.gz | 429.7 KB | Display | wwPDB validaton report |
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Full document | 2dri_full_validation.pdf.gz | 430.4 KB | Display | |
Data in XML | 2dri_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 2dri_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/2dri ftp://data.pdbj.org/pub/pdb/validation_reports/dr/2dri | 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
#1: Protein | Mass: 28507.424 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P02925 |
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#2: Sugar | ChemComp-RIP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.74 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.6 Å / Num. obs: 32471 / % possible obs: 95 % / Observed criterion σ(I): 1 / Num. measured all: 109138 / Rmerge(I) obs: 0.058 / Biso Wilson estimate: 24.9 Å2 |
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-Processing
Software |
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Refinement | Resolution: 1.6→7.5 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 1.6→7.5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.194 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.11 |