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Yorodumi- PDB-6hbm: Crystal structure of MSMEG_1712 from Mycobacterium smegmatis in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hbm | |||||||||
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Title | Crystal structure of MSMEG_1712 from Mycobacterium smegmatis in complex with alpha-L-arabinofuranose | |||||||||
Components | ABC transporter periplasmic-binding protein YtfQ | |||||||||
Keywords | SUGAR BINDING PROTEIN / periplasmic binding protein | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Mycobacterium smegmatis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å | |||||||||
Authors | Li, M. / Mueller, C. / Einsle, O. / Jessen-Trefzer, C. | |||||||||
Citation | Journal: Cell Chem Biol / Year: 2019 Title: Detection and Characterization of a Mycobacterial L-Arabinofuranose ABC Transporter Identified with a Rapid Lipoproteomics Protocol. Authors: Li, M. / Muller, C. / Frohlich, K. / Gorka, O. / Zhang, L. / Gross, O. / Schilling, O. / Einsle, O. / Jessen-Trefzer, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hbm.cif.gz | 226.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hbm.ent.gz | 181.9 KB | Display | PDB format |
PDBx/mmJSON format | 6hbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hbm_validation.pdf.gz | 462.2 KB | Display | wwPDB validaton report |
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Full document | 6hbm_full_validation.pdf.gz | 468.3 KB | Display | |
Data in XML | 6hbm_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 6hbm_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/6hbm ftp://data.pdbj.org/pub/pdb/validation_reports/hb/6hbm | HTTPS FTP |
-Related structure data
Related structure data | 6hb0SC 6hbdC 6hyhC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33830.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_1712 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QT50 #2: Chemical | ChemComp-ZN / #3: Sugar | #4: Water | ChemComp-HOH / | |
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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: 3.1 Å3/Da / Density % sol: 60.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris, pH 8.0 21 % PEG 400 0.325 M NaOAc 0.1 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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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 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→106.5 Å / Num. obs: 63068 / % possible obs: 92.9 % / Redundancy: 25.7 % / Biso Wilson estimate: 109.79 Å2 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.75→3.19 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HB0 Resolution: 2.76→28.95 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.861 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.606
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Displacement parameters | Biso mean: 96.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.49 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.76→28.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.76→3.14 Å / Total num. of bins used: 26
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