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Yorodumi- PDB-6bs5: Crystal structure of AMP-PNP-bound bacterial Get3-like A and B in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bs5 | ||||||
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Title | Crystal structure of AMP-PNP-bound bacterial Get3-like A and B in Mycobacterium tuberculosis | ||||||
Components |
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Keywords | UNKNOWN FUNCTION / Complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Li, H. / Hu, K. / Kovach, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Bacteriol. / Year: 2019 Title: Characterization of Guided Entry of Tail-Anchored Proteins 3 Homologues in Mycobacterium tuberculosis. Authors: Hu, K. / Jordan, A.T. / Zhang, S. / Dhabaria, A. / Kovach, A. / Rangel, M.V. / Ueberheide, B. / Li, H. / Darwin, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bs5.cif.gz | 142.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bs5.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 6bs5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bs5_validation.pdf.gz | 776.9 KB | Display | wwPDB validaton report |
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Full document | 6bs5_full_validation.pdf.gz | 789.2 KB | Display | |
Data in XML | 6bs5_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 6bs5_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/6bs5 ftp://data.pdbj.org/pub/pdb/validation_reports/bs/6bs5 | HTTPS FTP |
-Related structure data
Related structure data | 6bs3SC 6bs4C 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35893.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: Rv3679, MTV025.027 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WKX5 |
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#2: Protein | Mass: 42518.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: Rv3680 / Production host: Escherichia coli (E. coli) / References: UniProt: I6Y498 |
#3: Chemical | ChemComp-ANP / |
#4: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: PEG8000, calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.05969 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 20, 2017 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05969 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→28.282 Å / Num. obs: 18969 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.243 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 3.1→3.21 Å / Rmerge(I) obs: 0.958 / Num. unique obs: 2594 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6BS3 Resolution: 3.1→28.282 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→28.282 Å
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Refine LS restraints |
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LS refinement shell |
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