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Yorodumi- PDB-6x6b: Structure of the sulfate-bound form of ArrX from Chrysiogenes ars... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x6b | ||||||
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Title | Structure of the sulfate-bound form of ArrX from Chrysiogenes arsenatis | ||||||
Components | ArrX | ||||||
Keywords | SIGNALING PROTEIN / Periplasmic binding protein | ||||||
Biological species | Chrysiogenes arsenatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Maher, M.J. / Poddar, N. | ||||||
Citation | Journal: Biochemistry / Year: 2021 Title: Structural and Functional Investigation of the Periplasmic Arsenate-Binding Protein ArrX from Chrysiogenes arsenatis . Authors: Poddar, N. / Badilla, C. / Maghool, S. / Osborne, T.H. / Santini, J.M. / Maher, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x6b.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x6b.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 6x6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x6b_validation.pdf.gz | 728.6 KB | Display | wwPDB validaton report |
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Full document | 6x6b_full_validation.pdf.gz | 729.7 KB | Display | |
Data in XML | 6x6b_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 6x6b_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/6x6b ftp://data.pdbj.org/pub/pdb/validation_reports/x6/6x6b | HTTPS FTP |
-Related structure data
Related structure data | 6x8wC 6x9gC 6xabC 6xadC 6xl2C 7l22C 6eskS 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: 34338.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chrysiogenes arsenatis (bacteria) / Production host: Escherichia coli (E. coli) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-PG4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.05 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→45.7 Å / Num. obs: 29902 / % possible obs: 99.4 % / Redundancy: 12.9 % / CC1/2: 0.997 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.67→1.71 Å / Num. unique obs: 2161 / CC1/2: 0.524 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ESK Resolution: 1.67→45.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.582 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.098 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.458 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→45.7 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: 20
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