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- PDB-6xad: Structure of the formate-bound form of ArrX from Chrysiogenes ars... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xad | ||||||
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Title | Structure of the formate-bound form of ArrX from Chrysiogenes arsenatis | ||||||
![]() | ArrX | ||||||
![]() | SIGNALING PROTEIN / Periplasmic binding protein | ||||||
Function / homology | FORMIC ACID![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maher, M.J. / Poddar, N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.2 KB | Display | ![]() |
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PDB format | ![]() | 48.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.1 KB | Display | ![]() |
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Full document | ![]() | 433.3 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 17 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x6bSC ![]() 6x8wC ![]() 6x9gC ![]() 6xabC ![]() 6xl2C ![]() 7l22C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FMT / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.15 M magnesium formate dihydrate, 18% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→44.1 Å / Num. obs: 20100 / % possible obs: 98.8 % / Redundancy: 3.5 % / CC1/2: 0.995 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.89→1.94 Å / Num. unique obs: 1215 / CC1/2: 0.514 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6X6B Resolution: 1.893→44.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.795 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.145 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: 24.547 Å2
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Refinement step | Cycle: LAST / Resolution: 1.893→44.1 Å
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Refine LS restraints |
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LS refinement shell |
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