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Yorodumi- PDB-4q2m: Structure of the E. coli YajR Transporter YAM Domain Combined Iodine -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q2m | ||||||
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Title | Structure of the E. coli YajR Transporter YAM Domain Combined Iodine | ||||||
Components | Major facilitator superfamily MFS_1 | ||||||
Keywords | TRANSPORT PROTEIN / Feredoxin Fold / transporter | ||||||
Function / homology | Function and homology information transmembrane transporter activity / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.489 Å | ||||||
Authors | Zhang, X.C. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2014 Title: Atomic resolution structure of the E. coli YajR transporter YAM domain. Authors: Jiang, D. / Zhao, Y. / Fan, J. / Liu, X. / Wu, Y. / Feng, W. / Zhang, X.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q2m.cif.gz | 25.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q2m.ent.gz | 18.4 KB | Display | PDB format |
PDBx/mmJSON format | 4q2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/4q2m ftp://data.pdbj.org/pub/pdb/validation_reports/q2/4q2m | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 7858.906 Da / Num. of mol.: 1 / Fragment: YAM domain, UNP residues 388-454 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / BL21-DE3 / Gene: B21_00379, E. coli, ECBD_3234, ECD_00375, yajR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C6EL42, UniProt: A0A140NCX4*PLUS | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-IOD / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.61 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES (pH 7.5), 50mM CdSO4, 1.0M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 4, 2013 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.489→50 Å / Num. obs: 21855 / % possible obs: 96.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.49→1.54 Å / Redundancy: 6 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 6.1 / Num. unique all: 1229 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.489→23.078 Å / SU ML: 0.11 / σ(F): 1.38 / Phase error: 25.62 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.489→23.078 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: 8
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