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- PDB-1rpj: CRYSTAL STRUCTURE OF D-ALLOSE BINDING PROTEIN FROM ESCHERICHIA COLI -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rpj | |||||||||
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Title | CRYSTAL STRUCTURE OF D-ALLOSE BINDING PROTEIN FROM ESCHERICHIA COLI | |||||||||
![]() | PROTEIN (PRECURSOR OF PERIPLASMIC SUGAR RECEPTOR) | |||||||||
![]() | PERIPLASMIC SUGAR RECEPTOR | |||||||||
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 | ![]() ![]() | |||||||||
![]() | Chaudhuri, B. / 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. #1: ![]() Title: The D-Allose Operon of Escherichia Coli K-12 Authors: Kim, C. / Song, S. / Park, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.1 KB | Display | ![]() |
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PDB format | ![]() | 51.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.5 KB | Display | ![]() |
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Full document | ![]() | 446.7 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gubC ![]() 1gudC ![]() 2driS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30417.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#4: Sugar | ChemComp-ALL / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | ZINC SULFATE WAS ESSENTIAL FOR CRYSTALLIZATION AND BOTH ZINC AND SULFATE IONS COULD BE MODELLED IN ...ZINC SULFATE WAS ESSENTIAL FOR CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 41 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS 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 | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29.787 Å / Num. obs: 21163 / % possible obs: 96.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 17.07 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5 / % possible all: 93.6 |
Reflection shell | *PLUS % possible obs: 93.6 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DRI Resolution: 1.8→29 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: CNS WAS USED BEFORE REFMAC FOR REFINEMENT
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Displacement parameters | Biso mean: 11.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.194 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |