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- PDB-8tg1: Caldicellulosiruptor saccharolyticus periplasmic urea-binding protein -
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Open data
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Basic information
Entry | Database: PDB / ID: 8tg1 | ||||||
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Title | Caldicellulosiruptor saccharolyticus periplasmic urea-binding protein | ||||||
![]() | Extracellular ligand-binding receptor | ||||||
![]() | TRANSPORT PROTEIN / Periplasmic binding protein / UREA BINDING PROTEIN | ||||||
Function / homology | Urea ABC transporter, substrate-binding protein UrtA-like / Periplasmic binding protein domain / Leu/Ile/Val-binding protein / amino acid transport / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / BROMIDE ION / UREA / Extracellular ligand-binding receptor![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Allert, M.J. / Kumar, S. / Wang, Y. / Beese, L.S. / Hellinga, H.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-based functional analysis reveals multiple roles and widespread use of urea-binding proteins in nitrogen metabolism Authors: Allert, M.J. / Kumar, S. / Wang, Y. / Beese, L.S. / Hellinga, H.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.8 KB | Display | ![]() |
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PDB format | ![]() | 138.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 974.2 KB | Display | ![]() |
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Full document | ![]() | 976.6 KB | Display | |
Data in XML | ![]() | 37.6 KB | Display | |
Data in CIF | ![]() | 58.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1peaS 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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Unit cell |
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Components
#1: Protein | Mass: 43741.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Csac_2475 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-BR / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.62 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2M ammonium sulfate, 0.1M sodium acetate, 25% PEG 4000. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0162 Å / Relative weight: 1 |
Reflection | Resolution: 2.097→45.83 Å / Num. obs: 41757 / % possible obs: 99.55 % / Redundancy: 3.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.1671 / Rpim(I) all: 0.09547 / Net I/σ(I): 8.73 |
Reflection shell | Resolution: 2.097→2.172 Å / Rmerge(I) obs: 0.7254 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 4073 / CC1/2: 0.809 / Rpim(I) all: 0.4144 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1pea Resolution: 2.097→45.83 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.097→45.83 Å
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Refine LS restraints |
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LS refinement shell |
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