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Yorodumi- PDB-6xhh: Far-red absorbing dark state of JSC1_58120g3 with bound 18-1, 18-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xhh | ||||||||||||
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Title | Far-red absorbing dark state of JSC1_58120g3 with bound 18-1, 18-2 dihydrobiliverdin IXa (DHBV), the native chromophore precursor | ||||||||||||
Components | JSC1_58120g3 | ||||||||||||
Keywords | SIGNALING PROTEIN / Cyanobacteriochrome GAF Domain Phytochrome-superfamily 18-1 / 18-2 Dihydrobiliverdin | ||||||||||||
Function / homology | mesobiliverdin IX(alpha) Function and homology information | ||||||||||||
Biological species | [Leptolyngbya] sp. JSC-1 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||||||||
Authors | Moreno, M.V. / Rockwell, N.C. / Fisher, A.J. / Lagarias, J.C. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: A far-red cyanobacteriochrome lineage specific for verdins. Authors: Moreno, M.V. / Rockwell, N.C. / Mora, M. / Fisher, A.J. / Lagarias, J.C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xhh.cif.gz | 100.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xhh.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 6xhh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xhh_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6xhh_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6xhh_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 6xhh_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/6xhh ftp://data.pdbj.org/pub/pdb/validation_reports/xh/6xhh | HTTPS FTP |
-Related structure data
Related structure data | 6xhgC 3w2zS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21026.643 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) [Leptolyngbya] sp. JSC-1 (bacteria) / Plasmid: pBAD-CBD Details (production host): intein-CBD tag, Ampicillin resistance Production host: Escherichia coli (E. coli) / Strain (production host): LMG 194 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Nonpolymer details | The added ligand was 18-1, 18-2 dihydrobiliverdin IXa that forms a covalent adduct with the ...The added ligand was 18-1, 18-2 dihydrobiliverdin IXa that forms a covalent adduct with the protein, which is equivalent to a mesobiliverdin IXa moiety bonded to Cys636. | |
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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: 2.02 Å3/Da / Density % sol: 39.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.25 M Ammonium Citrate, 25% (v/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.5→36.68 Å / Num. obs: 44374 / % possible obs: 84.3 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.031 / Rrim(I) all: 0.06 / Net I/σ(I): 13.8 / Num. measured all: 169907 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.8 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W2Z Resolution: 1.5→30.521 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.47
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.58 Å2 / Biso mean: 20.7147 Å2 / Biso min: 7.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→30.521 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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