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Yorodumi- PDB-8fq9: Crystal structure of a ligand-bound cation-site mutant D55C of a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fq9 | ||||||
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Title | Crystal structure of a ligand-bound cation-site mutant D55C of a melibiose transporter | ||||||
Components | Melibiose permease | ||||||
Keywords | MEMBRANE PROTEIN / Cation-coupled symporter / sugar transporter / MFS Na+-coupled transporter | ||||||
Function / homology | Function and homology information : / symporter activity / sodium ion transport / carbohydrate transport / plasma membrane Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Guan, L. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of a ligand-bound cation-site mutant D55C of a melibiose transporter Authors: Guan, L. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Zwart, P.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fq9.cif.gz | 331.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fq9.ent.gz | 229.1 KB | Display | PDB format |
PDBx/mmJSON format | 8fq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fq9_validation.pdf.gz | 974.6 KB | Display | wwPDB validaton report |
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Full document | 8fq9_full_validation.pdf.gz | 989.6 KB | Display | |
Data in XML | 8fq9_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 8fq9_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/8fq9 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/8fq9 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: D55C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: melB, STM4299 / Organ: Salmonella typhimurium / Production host: Escherichia coli (E. coli) / Strain (production host): DW2 / References: UniProt: P30878 |
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#2: Chemical | ChemComp-1PE / |
#3: 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: 4.61 Å3/Da / Density % sol: 73.33 % |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MES, 100 mM, PH 6.5 NaCl, 100 mM CaCl, 50 mM PEG400, 32% |
-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 PILATUS 6M / Detector: PIXEL / Date: May 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 3→25 Å / Num. obs: 19790 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.048 / Rrim(I) all: 0.125 / Χ2: 1.02 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 3.18→3.4 Å / Redundancy: 20.1 % / Rmerge(I) obs: 1.705 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2982 / CC1/2: 0.728 / Rpim(I) all: 0.398 / Rrim(I) all: 1.791 / Χ2: 1.02 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→24.56 Å / SU ML: 0.4464 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.3952 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: 114.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→24.56 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: -56.3807391713 Å / Origin y: 3.82089233665 Å / Origin z: 11.1438046751 Å
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Refinement TLS group | Selection details: all |