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Yorodumi- PDB-6dxi: Crystal structure of H-NOX protein from Nostoc sp V52W/L67W doubl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dxi | ||||||||||||||||||
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Title | Crystal structure of H-NOX protein from Nostoc sp V52W/L67W double-mutant. | ||||||||||||||||||
Components | H-NOX | ||||||||||||||||||
Keywords | SIGNALING PROTEIN / NO-sensing / ferrous heme / cyanobacteria | ||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||
Biological species | Nostoc sp. (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å | ||||||||||||||||||
Authors | Weichsel, A. / Kievenaar, J.A. / Montfort, W.R. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: to be published Title: Structure of H-NOX domain from cyanobacteria Nostoc sp Authors: Kievenaar, J.A. / Croft, J.T. / Li, J. / Feng, C. / Weichsel, A. / Montfort, W.R. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dxi.cif.gz | 54.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dxi.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 6dxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/6dxi ftp://data.pdbj.org/pub/pdb/validation_reports/dx/6dxi | HTTPS FTP |
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-Related structure data
Related structure data | 6mx5C 6dx6 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: 21473.979 Da / Num. of mol.: 1 / Mutation: V52W, L67W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (bacteria) / Plasmid: pET-21b / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): rosetta / References: UniProt: A0A1Z4KG06, UniProt: Q8YUQ7*PLUS |
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#2: Chemical | ChemComp-HEM / |
#3: 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: 3 Å3/Da / Density % sol: 59 % / Description: hexagonal rod |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: sodium phosphate, potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2018 Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 8033 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 47.8 Å2 / Rmerge(I) obs: 0.139 / Χ2: 0.96 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 964 / Χ2: 0.89 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6DX6 6dx6 Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.905 / SU B: 14.709 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R: 0.584 / ESU R Free: 0.313 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.451 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→30 Å
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Refine LS restraints |
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