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Yorodumi- PDB-6zgu: Crystal structure of a MFS transporter with bound 3-(2-methylphen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zgu | ||||||
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Title | Crystal structure of a MFS transporter with bound 3-(2-methylphenyl)propanoic acid at 2.41 Angstroem resolution | ||||||
Components | L-lactate transporter | ||||||
Keywords | MEMBRANE PROTEIN / L-lactate transporter / monocarboxylate transporter / SLC16 family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Syntrophobacter fumaroxidans MPOB (syntrophic propionate-oxidizing bacterium DSM 10017) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.18 Å | ||||||
Authors | Kalbermatter, D. / Bosshart, P. / Bonetti, S. / Fotiadis, D. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Commun Chem / Year: 2021 Title: The making of a potent L-lactate transport inhibitor Authors: Bosshart, P.D. / Kalbermatter, D. / Bonetti, S. / Fotiadis, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zgu.cif.gz | 305.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zgu.ent.gz | 249.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zgu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zgu_validation.pdf.gz | 977.5 KB | Display | wwPDB validaton report |
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Full document | 6zgu_full_validation.pdf.gz | 1010.8 KB | Display | |
Data in XML | 6zgu_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 6zgu_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/6zgu ftp://data.pdbj.org/pub/pdb/validation_reports/zg/6zgu | HTTPS FTP |
-Related structure data
Related structure data | 6zgrC 6zgsC 6zgtC 6g9xS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 44799.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Syntrophobacter fumaroxidans MPOB (syntrophic propionate-oxidizing bacterium DSM 10017) Gene: Sfum_3364 / Plasmid: pZUDF21-rbs-3C-10His / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0LNN5 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.89 % / Mosaicity: 0.09 ° |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: zinc bromide, HEPES, jeffamine ED-2003 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2019 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.18→49.44 Å / Num. obs: 66703 / % possible obs: 100 % / Redundancy: 32.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.031 / Rrim(I) all: 0.164 / Net I/σ(I): 18.9 / Num. measured all: 2143898 / Scaling rejects: 99709 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G9X Resolution: 2.18→14.968 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.76 / Stereochemistry target values: ML
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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 max: 217.31 Å2 / Biso mean: 97.0232 Å2 / Biso min: 31.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.18→14.968 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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