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Yorodumi- PDB-1apb: A PRO TO GLY MUTATION IN THE HINGE OF THE ARABINOSE-BINDING PROTE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1apb | |||||||||
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Title | A PRO TO GLY MUTATION IN THE HINGE OF THE ARABINOSE-BINDING PROTEIN ENHANCES BINDING AND ALTERS SPECIFICITY: SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES | |||||||||
Components | L-ARABINOSE-BINDING PROTEIN | |||||||||
Keywords | BINDING PROTEINS | |||||||||
Function / homology | Function and homology information L-arabinose transmembrane transport / ABC-type monosaccharide transporter activity / monosaccharide binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / carbohydrate binding / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.76 Å | |||||||||
Authors | Vermersch, P.S. / Tesmer, J.J.G. / Quiocho, F.A. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1990 Title: A Pro to Gly mutation in the hinge of the arabinose-binding protein enhances binding and alters specificity. Sugar-binding and crystallographic studies. Authors: Vermersch, P.S. / Tesmer, J.J. / Lemon, D.D. / Quiocho, F.A. #1: Journal: Nature / Year: 1989 Title: Substrate Specificity and Affinity of a Protein Modulated by Bound Water Molecules Authors: Quiocho, F.A. / Wilson, D.K. / Vyas, N.K. #2: Journal: Nature / Year: 1984 Title: Novel Stereospecificity of the L-Arabinose-Binding Protein Authors: Quiocho, F.A. / Vyas, N.K. #3: Journal: J.Biol.Chem. / Year: 1982 Title: Hinge-Bending in L-Arabinose-Binding Protein. The "Venus'S-Flytrap" Model Authors: Mao, B. / Pear, M.R. / Mccammon, J.A. / Quiocho, F.A. #4: Journal: J.Mol.Biol. / Year: 1981 Title: Structure of the L-Arabinose-Binding Protein from Escherichia Coli at 2.4 Angstroms Resolution Authors: Gilliland, G.L. / Quiocho, F.A. #5: Journal: J.Biol.Chem. / Year: 1981 Title: L-Arabinose-Binding Protein-Sugar Complex at 2.4 Angstroms Resolution. Stereochemistry and Evidence for a Structural Change Authors: Newcomer, M.E. / Gilliand, G.L. / Quiocho, F.A. #6: Journal: J.Biol.Chem. / Year: 1981 Title: The Radius of Gyration of L-Arabinose-Binding Protein Decreases Upon Binding of Ligand Authors: Newcomer, M.E. / Lewis, B.A. / Quiocho, F.A. #7: Journal: J.Biol.Chem. / Year: 1979 Title: The Thiol Group of the L-Arabinose-Binding Protein. Chromophoric Labeling and Chemical Identification of the Sugar-Binding Site Authors: Miller /III, D.M. / Newcomer, M.E. / Quiocho, F.A. #8: Journal: J.Biol.Chem. / Year: 1979 Title: Location of the Sugar-Binding Site of L-Arabinose-Binding Protein. Sugar Derivative Syntheses, Sugar Binding Specificity, and Difference Fourier Analyses Authors: Newcomer, M.E. / Miller /III, D.M. / Quiocho, F.A. #9: Journal: J.Biol.Chem. / Year: 1977 Title: The 2.8-Angstroms Resolution Structure of the L-Arabinose-Binding Protein from Escherichia Coli Authors: Quiocho, F.A. / Gilliland, G.L. / Phillips Jr., G.N. #10: Journal: Proc.Natl.Acad.Sci.USA / Year: 1976 Title: Structure of L-Arabinose-Binding Protein from Escherichia Coli at 5 Angstroms Resolution and Preliminary Results at 3.5 Angstroms Authors: Phillips Jr., G.N. / Mahajan, V.K. / Siu, A.K.Q. / 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 | 1apb.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1apb.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 1apb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1apb_validation.pdf.gz | 400.9 KB | Display | wwPDB validaton report |
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Full document | 1apb_full_validation.pdf.gz | 406.3 KB | Display | |
Data in XML | 1apb_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1apb_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/1apb ftp://data.pdbj.org/pub/pdb/validation_reports/ap/1apb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: SEE REMARK 5. |
-Components
#1: Protein | Mass: 33210.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P02924 |
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#2: Sugar | ChemComp-FCA / |
#3: Sugar | ChemComp-FCB / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | SINCE IT HAS BEEN SHOWN THAT ABP CAN BIND EITHER ALPHA OR BETA ANOMERS OF D-FUCOSE WITH ALMOST ...SINCE IT HAS BEEN SHOWN THAT ABP CAN BIND EITHER ALPHA OR BETA ANOMERS OF D-FUCOSE WITH ALMOST EQUAL AFFINITY, BOTH ARE PROVIDED IN THE SAME SITE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.28 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.76 Å / Num. obs: 25278 / % possible obs: 79 % / Num. measured all: 68318 / Rmerge F obs: 0.0562 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.76→8 Å /
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Refinement step | Cycle: LAST / Resolution: 1.76→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.76 Å / Lowest resolution: 8 Å / σ(I): 2 / Rfactor obs: 0.192 / Num. reflection obs: 24421 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |