+Open data
-Basic information
Entry | Database: PDB / ID: 7l16 | |||||||||
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Title | Crystal structure of sugar-bound melibiose permease MelB | |||||||||
Components | Melibiose carrier protein | |||||||||
Keywords | TRANSPORT PROTEIN / MFS-fold / galactoside binding / secondary active transport / MelB | |||||||||
Function / homology | Function and homology information : / symporter activity / sodium ion transport / carbohydrate transport / plasma membrane Similarity search - Function | |||||||||
Biological species | Salmonella typhimurium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | |||||||||
Authors | Guan, L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Commun Biol / Year: 2021 Title: X-ray crystallography reveals molecular recognition mechanism for sugar binding in a melibiose transporter MelB. Authors: Guan, L. / Hariharan, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l16.cif.gz | 327.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l16.ent.gz | 227 KB | Display | PDB format |
PDBx/mmJSON format | 7l16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7l16_validation.pdf.gz | 785.5 KB | Display | wwPDB validaton report |
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Full document | 7l16_full_validation.pdf.gz | 792 KB | Display | |
Data in XML | 7l16_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 7l16_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/7l16 ftp://data.pdbj.org/pub/pdb/validation_reports/l1/7l16 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54092.496 Da / Num. of mol.: 1 / Mutation: D59C, M5L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Cell line: LT2 / Gene: melB, STM4299 / Plasmid: pK95 / Details (production host): pK95 / Production host: Escherichia coli (E. coli) / Strain (production host): DW2 / Variant (production host): melBlacYZ / References: UniProt: P30878 |
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#2: Sugar | ChemComp-LMO / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.62 Å3/Da / Density % sol: 73.35 % / Description: Rod |
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Crystal grow | Temperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 50 mM BaCl2, 50 mM CaCl2, 100 mM Tris-HCl, pH 8.5, 29-32% PEG 400, 0.015% DDMB, 10% PEG3350 PH range: 6.5 - 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: May 19, 2018 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→29.35 Å / Num. obs: 16973 / % possible obs: 99.9 % / Redundancy: 19.2 % / Biso Wilson estimate: 96.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.046 / Rrim(I) all: 0.146 / Χ2: 1.12 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 3.15→3.37 Å / Rmerge(I) obs: 1.1463 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3080 / CC1/2: 0.788 / Rpim(I) all: 0.477 / Rrim(I) all: 1.539 / Χ2: 0.89 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MelB D59C with aNPG submitted Resolution: 3.15→29.35 Å / SU ML: 0.3867 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.802 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: 103.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→29.35 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -25.0960065607 Å / Origin y: 50.6654286047 Å / Origin z: -6.13688007058 Å
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Refinement TLS group | Selection details: all |