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Yorodumi- PDB-2o0c: Crystal structure of the H-NOX domain from Nostoc sp. PCC 7120 co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o0c | ||||||
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Title | Crystal structure of the H-NOX domain from Nostoc sp. PCC 7120 complexed to NO | ||||||
Components | Alr2278 protein | ||||||
Keywords | SIGNALING PROTEIN / heme / NO / CO / guanylyl cyclase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nostoc sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Ma, X. / van den Akker, F. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: NO and CO differentially activate soluble guanylyl cyclase via a heme pivot-bend mechanism. Authors: Ma, X. / Sayed, N. / Beuve, A. / van den Akker, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o0c.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o0c.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 2o0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/2o0c ftp://data.pdbj.org/pub/pdb/validation_reports/o0/2o0c | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 21213.643 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr2278 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8YUQ7 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.7 Å3/Da / Density % sol: 66.8 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 1.4M tri-sodium citrate dihydrate, pH 5.6-6.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 18960 / % possible obs: 96.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2 / Num. unique all: 2925 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→37.27 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.986 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.371 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.238 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→37.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.672 Å / Total num. of bins used: 20
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