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Yorodumi- PDB-4gj4: The Crystal Structure of the soluble Guanylate Cyclase PAS alpha ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gj4 | ||||||
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Title | The Crystal Structure of the soluble Guanylate Cyclase PAS alpha domain from Manduca sexta | ||||||
Components | Soluble guanylyl cyclase alpha-1 subunit | ||||||
Keywords | LYASE / Nitric Oxide / cGMP / YC-1 / PAS Domain / PAS Fold / Allosteric Regulation | ||||||
Function / homology | Function and homology information guanylate cyclase / guanylate cyclase complex, soluble / guanylate cyclase activity / response to oxygen levels / cGMP-mediated signaling / heme binding / GTP binding Similarity search - Function | ||||||
Biological species | Manduca sexta (tobacco hornworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Purohit, R. / Montfort, W.R. / Weichsel, A. | ||||||
Citation | Journal: Protein Sci. / Year: 2013 Title: Crystal structure of the Alpha subunit PAS domain from soluble guanylyl cyclase. Authors: Purohit, R. / 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 | 4gj4.cif.gz | 200.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gj4.ent.gz | 163.3 KB | Display | PDB format |
PDBx/mmJSON format | 4gj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/4gj4 ftp://data.pdbj.org/pub/pdb/validation_reports/gj/4gj4 | HTTPS FTP |
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-Related structure data
Related structure data | 2p04S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13821.136 Da / Num. of mol.: 4 / Fragment: sGC PAS alpha Domain residues 279-404 / Mutation: C285A, C352A, C374A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Manduca sexta (tobacco hornworm) / Plasmid: pETHSUL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: O77105, guanylate cyclase #2: Chemical | ChemComp-SO4 / #3: 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: 2.52 Å3/Da / Density % sol: 51.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 1.5 M Lithium Sulfate, 0.1 M Hepes, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 7, 2012 / Details: Rh coated flat mirror |
Radiation | Monochromator: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→23.7 Å / Num. all: 52047 / Num. obs: 52047 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.75 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 8.56 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5122 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2P04 Resolution: 1.8→23.15 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.651 / SU ML: 0.098 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.124 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.363 Å2
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Refine analyze | Luzzati coordinate error obs: 0.294 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→23.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 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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