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Open data
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Basic information
Entry | Database: PDB / ID: 1urp | ||||||
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Title | D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI | ||||||
![]() | D-RIBOSE-BINDING PROTEIN | ||||||
![]() | TRANSPORT / CHEMOTAXIS / PERIPLASM | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bjorkman, A.J. / Mowbray, S.L. | ||||||
![]() | ![]() Title: Multiple open forms of ribose-binding protein trace the path of its conformational change. Authors: Bjorkman, A.J. / Mowbray, S.L. #1: ![]() Title: Identical Mutations at Corresponding Positions in Two Homologous Proteins with Nonidentical Effects Authors: Bjorkman, A.J. / Binnie, R.A. / Cole, L.B. / Zhang, H. / Hermodson, M.A. / Mowbray, S.L. #2: ![]() 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. #3: ![]() Title: 1.7 A X-Ray Structure of the Periplasmic Ribose Receptor from Escherichia Coli Authors: Mowbray, S.L. / Cole, L.B. #4: ![]() Title: Functional Mapping of the Surface of Escherichia Coli Ribose-Binding Protein: Mutations that Affect Chemotaxis and Transport Authors: Binnie, R.A. / Zhang, H. / Mowbray, S. / Hermodson, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.8 KB | Display | ![]() |
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PDB format | ![]() | 165.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.6 KB | Display | ![]() |
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Full document | ![]() | 465.6 KB | Display | |
Data in XML | ![]() | 39 KB | Display | |
Data in CIF | ![]() | 53.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 28507.424 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.81 % Description: RESOLUTION LIMITS 8-4 ANGSTROMS IN THE SEARCHES. | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5 Details: CRYSTALS WERE OBTAINED FROM SOLUTIONS OF 7.5 - 15 MG/ML RBP, 21% PEG4000, 50-100 MM SODIUM CITRATE, PH 4, 5% GLYCEROL, BY HANGING DROP VAPOUR DIFFUSION., pH 5.0, vapor diffusion - hanging drop | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9123 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 36827 / % possible obs: 90.7 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 4.6 / % possible all: 79.1 |
Reflection shell | *PLUS % possible obs: 79.1 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY FOR LIGAND-FREE MUTANT RBP, MOLECULE B. Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 32.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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