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- PDB-3omb: Crystal structure of extracellular solute-binding protein from Bi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3omb | ||||||
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Title | Crystal structure of extracellular solute-binding protein from Bifidobacterium longum subsp. infantis | ||||||
![]() | Extracellular solute-binding protein, family 1 | ||||||
![]() | TRANSPORT PROTEIN / PSI-2 / Midwest Center for Structural Genomics / Protein Structure Initiative / MCSG / transporter | ||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Extracellular solute-binding protein, family 1![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chang, C. / Xu, X. / Chin, S. / Cui, H. / Dong, A. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Crystal structure of extracellular solute-binding protein from Bifidobacterium longum subsp. infantis Authors: Chang, C. / Xu, X. / Chin, S. / Cui, H. / Dong, A. / Savchenko, A. / Edwards, A. / Joachimiak, 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 | ![]() | 220.6 KB | Display | ![]() |
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PDB format | ![]() | 186.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.9 KB | Display | ![]() |
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Full document | ![]() | 423.4 KB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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: 59835.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15697 / DSM 20088 / NCTC 11817 / S12 / Gene: Blon_2351 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.44 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M Bis-Tris, 0.2M MgCl2, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2010 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 28267 / Num. obs: 28262 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1393 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.6 Å2 / Biso mean: 27.254 Å2 / Biso min: 8.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.097→2.151 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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