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- PDB-1gud: Hinge-bending motion of D-allose binding protein from Escherichia... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gud | ||||||
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Title | Hinge-bending motion of D-allose binding protein from Escherichia coli: three open conformations | ||||||
![]() | D-ALLOSE-BINDING PERIPLASMIC PROTEIN | ||||||
![]() | PERIPLASMIC BINDING PROTEIN / ALLOSE / HINGE BENDING / CONFORMATIONAL CHANGE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Magnusson, U. / Chaudhuri, B.N. / Ko, J. / Park, C. / Jones, T.A. / Mowbray, S.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.8 KB | Display | ![]() |
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PDB format | ![]() | 99.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.4 KB | Display | ![]() |
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Full document | ![]() | 436.7 KB | Display | |
Data in XML | ![]() | 26.3 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gubC ![]() 1rpjSC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30417.807 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.2 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.00 | ||||||||||||||||||||||||||||||||||||||||||
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: ![]() ![]() ![]() |
Detector | Date: Dec 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→35.58 Å / Num. obs: 8404 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.0093 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.036 / Mean I/σ(I) obs: 6.3 / % possible all: 100 |
Reflection | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.362 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RPJ Resolution: 1.71→70.71 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.875 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.105 / 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: 12.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→70.71 Å
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Refine LS restraints |
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