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Yorodumi- PDB-1gub: Hinge-bending motion of D-allose binding protein from Escherichia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gub | ||||||
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Title | Hinge-bending motion of D-allose binding protein from Escherichia coli: three open conformations | ||||||
Components | D-ALLOSE-BINDING PERIPLASMIC PROTEIN | ||||||
Keywords | SUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / PERIPLASMIC BINDING PROTEIN / ALLOSE / HINGE BENDING / CONFORMATIONAL CHANGE | ||||||
Function / homology | Function and homology information D-allose transmembrane transport / D-ribose transmembrane transport / monosaccharide binding / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Magnusson, U. / Chaudhuri, B.N. / Ko, J. / Park, C. / Jones, T.A. / Mowbray, S.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Structure of D-Allose Binding Protein from Escherichia Coli Bound to D-Allose at 1.8 A Resolution Authors: Chaudhuri, B.N. / Ko, J. / Park, C. / Jones, T.A. / 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 | 1gub.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gub.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 1gub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/1gub ftp://data.pdbj.org/pub/pdb/validation_reports/gu/1gub | HTTPS FTP |
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-Related structure data
Related structure data | 1gudC 1rpjSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 30417.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K12 / References: UniProt: P39265 |
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#2: Chemical | ChemComp-NI / |
#3: 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: 3.23 Å3/Da / Density % sol: 62 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9 / Details: pH 9.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.89 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→29 Å / Num. obs: 625 / % possible obs: 99.5 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.0094 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 3.08→3.16 Å / Rmerge(I) obs: 0.034 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 29 Å / Rmerge(I) obs: 0.094 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.338 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RPJ Resolution: 3.1→29.75 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.781 / SU B: 27.453 / SU ML: 0.503 / Cross valid method: THROUGHOUT / ESU R Free: 0.589 / 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: 34.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→29.75 Å
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Refine LS restraints |
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