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- PDB-8wch: Crystal structure of SAR11_0655 bound to a co-purified ligand, L-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8wch | ||||||
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Title | Crystal structure of SAR11_0655 bound to a co-purified ligand, L-pyroglutamate | ||||||
![]() | Probable Leu/Ile/Val-binding protein | ||||||
![]() | TRANSPORT PROTEIN / ABC transporter / solute-binding protein / periplasmic binding protein | ||||||
Function / homology | Leucine-binding protein domain / Periplasmic binding protein / Periplasmic binding protein-like I / PYROGLUTAMIC ACID / Probable Leu/Ile/Val-binding protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Clifton, B.E. / Laurino, P. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of SAR11_0655 bound to a co-purified ligand, L-pyroglutamate Authors: Clifton, B.E. / Laurino, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 436.7 KB | Display | ![]() |
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PDB format | ![]() | 272.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1019.1 KB | Display | ![]() |
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Full document | ![]() | 1010.9 KB | Display | |
Data in XML | ![]() | 35 KB | Display | |
Data in CIF | ![]() | 52.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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 on special symmetry positions |
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Components
#1: Protein | Mass: 45020.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: HTCC1062 / Gene: braC / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #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: 2.74 Å3/Da / Density % sol: 55.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 1.5 uL 0.1 M sodium citrate pH 3.5, 0.15 M lithium sulfate, 16% (w/v) PEG 6000 + 1.5 uL 12 mg/mL protein. Cryoprotected in 0.1 M sodium citrate pH 3.5, 0.15 M lithium sulfate, 16% (w/v) PEG ...Details: 1.5 uL 0.1 M sodium citrate pH 3.5, 0.15 M lithium sulfate, 16% (w/v) PEG 6000 + 1.5 uL 12 mg/mL protein. Cryoprotected in 0.1 M sodium citrate pH 3.5, 0.15 M lithium sulfate, 16% (w/v) PEG 6000, 30% (v/v) ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.519→43.846 Å / Num. obs: 146122 / % possible obs: 99.9 % / Redundancy: 20.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.136 / Net I/σ(I): 14.89 |
Reflection shell | Resolution: 1.52→1.61 Å / Rmerge(I) obs: 3.18 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 23258 / CC1/2: 0.506 / Rrim(I) all: 3.26 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: AlphaFold Resolution: 1.519→41.304 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.143 / SU B: 3.128 / SU ML: 0.048 / Average fsc free: 0.97 / Average fsc work: 0.9784 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.063 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.753 Å2
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Refinement step | Cycle: LAST / Resolution: 1.519→41.304 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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