+Open data
-Basic information
Entry | Database: PDB / ID: 4iae | ||||||
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Title | Crystal structure of BAY 60-2770 bound to nostoc H-NOX domain | ||||||
Components | Alr2278 protein | ||||||
Keywords | LYASE / activation / HNOX domain / Heme binding / NO binding | ||||||
Function / homology | Function and homology information guanylate cyclase complex, soluble / guanylate cyclase activity / response to oxygen levels / cGMP-mediated signaling / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Nostoc sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Kumar, V. / van den Akker, F. / Martin, F. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Insights into BAY 60-2770 Activation and S-Nitrosylation-Dependent Desensitization of Soluble Guanylyl Cyclase via Crystal Structures of Homologous Nostoc H-NOX Domain Complexes. Authors: Kumar, V. / Martin, F. / Hahn, M.G. / Schaefer, M. / Stamler, J.S. / Stasch, J.P. / 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 | 4iae.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iae.ent.gz | 69.3 KB | Display | PDB format |
PDBx/mmJSON format | 4iae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iae_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4iae_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4iae_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 4iae_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/4iae ftp://data.pdbj.org/pub/pdb/validation_reports/ia/4iae | HTTPS FTP |
-Related structure data
Related structure data | 4iahC 4iamC 2o09S 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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Unit cell |
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-Components
#1: Protein | Mass: 21181.578 Da / Num. of mol.: 2 / Fragment: HNOX domain / Mutation: C139A Source method: isolated from a genetically manipulated source Details: similar to soluble guanylyl cyclase beta subunit / Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr2278 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8YUQ7, guanylate cyclase #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: 3.56 Å3/Da / Density % sol: 65.49 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 18, 2010 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→86.2 Å / Num. all: 36315 / Num. obs: 36251 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 34.4 Å2 / Rsym value: 0.048 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.05→2.12 Å / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2O09 Resolution: 2.05→86.2 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.359 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 1.72 / ESU R: 0.026 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.373 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→86.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.102 Å / Total num. of bins used: 20
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