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- PDB-6lu3: Crystal structure of a substrate binding protein from Microbacter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6lu3 | ||||||
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Title | Crystal structure of a substrate binding protein from Microbacterium hydrocarbonoxydans complexed with 4-hydroxybenzoate hydrazide | ||||||
![]() | Substrate binding protein | ||||||
![]() | TRANSPORT PROTEIN / Complex | ||||||
Function / homology | 4-oxidanylbenzohydrazide![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shimamura, K. / Akiyama, T. / Yokoyama, K. / Takenoya, M. / Ito, S. / Sasaki, Y. / Yajima, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of substrate recognition by the substrate binding protein (SBP) of a hydrazide transporter, obtained from Microbacterium hydrocarbonoxydans. Authors: Shimamura, K. / Akiyama, T. / Yokoyama, K. / Takenoya, M. / Ito, S. / Sasaki, Y. / Yajima, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.7 KB | Display | ![]() |
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PDB format | ![]() | 80.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 692.4 KB | Display | ![]() |
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Full document | ![]() | 692.8 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 28.5 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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Unit cell |
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Components
#1: Protein | Mass: 53585.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HDH / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
Sequence details | AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS GAT74979 FOR THE PROTEIN. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium acetate 0.1 M sodium cacodylate, pH 7.5 30% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 25212 / % possible obs: 98.9 % / Redundancy: 5.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.203 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1252 / CC1/2: 0.756 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.864 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→47.314 Å
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Refine LS restraints |
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LS refinement shell |
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