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Yorodumi- PDB-3uvj: Crystal structure of the catalytic domain of the heterodimeric hu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uvj | ||||||
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Title | Crystal structure of the catalytic domain of the heterodimeric human soluble guanylate cyclase 1. | ||||||
Components |
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Keywords | LYASE / Nitric Oxide / Structural Genomics / Structural Genomics Consortium / SGC / CGMP BIOSYNTHESIS / GTP binding METAL-BINDING / NUCLEOTIDE-BINDING / Cystol | ||||||
Function / homology | Function and homology information retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission / cytidylate cyclase activity / trans-synaptic signaling by nitric oxide, modulating synaptic transmission / guanylate cyclase / guanylate cyclase complex, soluble / cGMP biosynthetic process / guanylate cyclase activity / presynaptic active zone cytoplasmic component / response to oxygen levels / Nitric oxide stimulates guanylate cyclase ...retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission / cytidylate cyclase activity / trans-synaptic signaling by nitric oxide, modulating synaptic transmission / guanylate cyclase / guanylate cyclase complex, soluble / cGMP biosynthetic process / guanylate cyclase activity / presynaptic active zone cytoplasmic component / response to oxygen levels / Nitric oxide stimulates guanylate cyclase / relaxation of vascular associated smooth muscle / adenylate cyclase activity / blood circulation / cellular response to nitric oxide / positive regulation of nitric oxide mediated signal transduction / cGMP-mediated signaling / Smooth Muscle Contraction / GABA-ergic synapse / nitric oxide mediated signal transduction / nitric oxide-cGMP-mediated signaling / regulation of blood pressure / Hsp90 protein binding / signaling receptor activity / glutamatergic synapse / heme binding / protein-containing complex binding / GTP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Allerston, C.K. / Berridge, G. / Chalk, R. / Cooper, C.D.O. / Savitsky, P. / Vollmar, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. ...Allerston, C.K. / Berridge, G. / Chalk, R. / Cooper, C.D.O. / Savitsky, P. / Vollmar, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Crystal structures of the catalytic domain of human soluble guanylate cyclase. Authors: Allerston, C.K. / von Delft, F. / Gileadi, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uvj.cif.gz | 316.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uvj.ent.gz | 254.9 KB | Display | PDB format |
PDBx/mmJSON format | 3uvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uvj_validation.pdf.gz | 465.8 KB | Display | wwPDB validaton report |
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Full document | 3uvj_full_validation.pdf.gz | 467.4 KB | Display | |
Data in XML | 3uvj_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 3uvj_validation.cif.gz | 47.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/3uvj ftp://data.pdbj.org/pub/pdb/validation_reports/uv/3uvj | HTTPS FTP |
-Related 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: 24713.471 Da / Num. of mol.: 2 Fragment: soluble guanylate cyclase alpha-1 catalytic domain, UNP residues 468-690 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GUC1A3, GUCSA3, GUCY1A1, GUCY1A3 / Plasmid: pNH-TrxT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-Chaperones / References: UniProt: Q02108, guanylate cyclase #2: Protein | Mass: 24818.244 Da / Num. of mol.: 2 Fragment: soluble guanylate cyclase beta-1 catalytic domain, UNP residues 408-619 Mutation: G476C, C541S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GUCY1B3, GUC1B3, GUCSB3, GUCY1B1 / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-Chaperones / References: UniProt: Q02153, guanylate cyclase #3: Chemical | ChemComp-EDO / #4: Chemical | #5: 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: 1.98 Å3/Da / Density % sol: 37.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.05M KH2PO4 20% PEG 8000, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.968627 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2011 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968627 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→51.5 Å / Num. all: 47912 / Num. obs: 45874 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 36.79 Å2 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.08→2.16 Å / Redundancy: 3.3 % / Num. unique all: 6967 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→51.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.9389 / SU R Cruickshank DPI: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 39.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→51.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.13 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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