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Yorodumi- PDB-6m2l: Crystal structure of Plasmodium falciparum hexose transporter PfH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m2l | |||||||||
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Title | Crystal structure of Plasmodium falciparum hexose transporter PfHT1 bound with C3361 | |||||||||
Components | Hexose transporter 1 | |||||||||
Keywords | TRANSPORT PROTEIN / MFS / hexose transporter / inhibitor / Plasmodium falciparum | |||||||||
Function / homology | Function and homology information dehydroascorbic acid transport / D-glucose transmembrane transporter activity / glucose import / membrane Similarity search - Function | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | |||||||||
Authors | Jiang, X. / Yuan, Y.Y. / Zhang, S. / Wang, N. / Yan, C.Y. / Yan, N. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell / Year: 2020 Title: Structural Basis for Blocking Sugar Uptake into the Malaria Parasite Plasmodium falciparum. Authors: Jiang, X. / Yuan, Y. / Huang, J. / Zhang, S. / Luo, S. / Wang, N. / Pu, D. / Zhao, N. / Tang, Q. / Hirata, K. / Yang, X. / Jiao, Y. / Sakata-Kato, T. / Wu, J.W. / Yan, C. / Kato, N. / Yin, H. / Yan, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m2l.cif.gz | 355.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m2l.ent.gz | 293.1 KB | Display | PDB format |
PDBx/mmJSON format | 6m2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m2l_validation.pdf.gz | 816.6 KB | Display | wwPDB validaton report |
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Full document | 6m2l_full_validation.pdf.gz | 810.8 KB | Display | |
Data in XML | 6m2l_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 6m2l_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/6m2l ftp://data.pdbj.org/pub/pdb/validation_reports/m2/6m2l | HTTPS FTP |
-Related structure data
Related structure data | 6m20C 4zw9S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 56468.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: ht1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O97467 #2: Chemical | 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: 2.88 Å3/Da / Density % sol: 57.34 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.2 Details: 0.1 M NH4Cl, 0.1 M Na3Citrate pH 5.2, 28% PEG500MME |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→50 Å / Num. obs: 14879 / % possible obs: 99.8 % / Redundancy: 82.38 % / CC1/2: 0.998 / Net I/σ(I): 10.69 |
Reflection shell | Resolution: 3.7→3.9 Å / Num. unique obs: 2116 / CC1/2: 0.869 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZW9 Resolution: 3.7→19.959 Å / SU ML: 0.81 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 42.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 330.56 Å2 / Biso mean: 113.99 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.7→19.959 Å
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Refine LS restraints |
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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 / Origin x: -23.3925 Å / Origin y: -74.6374 Å / Origin z: 0.0634 Å
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Refinement TLS group | Selection details: all |