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- PDB-7pu4: Crystal structure of the dimer RBP-N and RBP-Trunc from Thermotog... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pu4 | ||||||
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Title | Crystal structure of the dimer RBP-N and RBP-Trunc from Thermotoga maritima Ribose Binding Protein | ||||||
![]() | (Ribose ABC transporter, periplasmic ribose-binding protein) x 2 | ||||||
![]() | SUGAR BINDING PROTEIN / Periplasmic Binding Protein / Substrate Binding Protein / Ribose / ligand binding | ||||||
Function / homology | Periplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / carbohydrate binding / Ribose ABC transporter, periplasmic ribose-binding protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Romero-Romero, S. / Michel, F. / Hocker, B. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Retracing the evolution of a modern periplasmic binding protein. Authors: Michel, F. / Romero-Romero, S. / Hocker, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 284 KB | Display | ![]() |
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PDB format | ![]() | 190.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.4 KB | Display | ![]() |
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Full document | ![]() | 463 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 36.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fn9S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Unit cell |
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Components
#1: Protein | Mass: 14873.854 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Chain A (RBP-N) & B (RBP-Trunc) form a dimer reconstructing the canonical Ribose Binding Protein Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8 Gene: TM_0958 / Plasmid: pET21b(+) / Production host: ![]() ![]() #2: Protein | Mass: 21522.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Chain A (RBP-N) & B (RBP-Trunc) form a dimer reconstructing the canonical Ribose Binding Protein Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8 Gene: TM_0958 / Plasmid: pET21b(+) / Production host: ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.7 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH: 7.5, PEG 20000 15% w/v, RBP-N and RBP-Trunc equimolarly mixed at 0.5 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 26, 2021 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→39.01 Å / Num. obs: 64629 / % possible obs: 99.76 % / Redundancy: 13.3 % / Biso Wilson estimate: 30.55 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1218 / Rpim(I) all: 0.03456 / Rrim(I) all: 0.1267 / Net I/σ(I): 14.25 |
Reflection shell | Resolution: 1.69→1.75 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 6298 / CC1/2: 0.318 / CC star: 0.695 / Rpim(I) all: 1.104 / Rrim(I) all: 1.196 / % possible all: 98.39 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FN9 Resolution: 1.69→39.01 Å / SU ML: 0.3135 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.7574 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→39.01 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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