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- PDB-2wz1: STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN SOLUBLE GUANYLATE CYCL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wz1 | ||||||
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Title | STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN SOLUBLE GUANYLATE CYCLASE 1 BETA 3. | ||||||
![]() | GUANYLATE CYCLASE SOLUBLE SUBUNIT BETA-1 | ||||||
![]() | LYASE / GUCY1 / METAL-BINDING / CGMP BIOSYNTHESIS / NUCLEOTIDE-BINDING / CYCLASE / GUCY1B3 / GTP-BINDING | ||||||
Function / homology | ![]() 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 / adenylate cyclase activity ...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 / adenylate cyclase activity / blood circulation / cGMP-mediated signaling / Smooth Muscle Contraction / cellular response to nitric oxide / nitric oxide mediated signal transduction / nitric oxide-cGMP-mediated signaling / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Allerston, C.K. / Cooper, C.D.O. / Muniz, J. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
![]() | ![]() Title: Crystal Structures of the Catalytic Domain of Human Soluble Guanylate Cyclase. Authors: Allerston, C.K. / von Delft, F. / Gileadi, O. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.6 KB | Display | ![]() |
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PDB format | ![]() | 74.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 446.3 KB | Display | ![]() |
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Full document | ![]() | 447.4 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3uvjC ![]() 3et6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.94655, -0.08878, 0.3101), Vector: |
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Components
#1: Protein | Mass: 24657.020 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 994-1205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.45 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.5 Details: PROTEIN WAS CONCENTRATED TO 12 MG/ML IN PURIFICATION BUFFER (10MM HEPES, 500MM NACL, 5% GLYCEROL, 10% GALACTOSE, 0.5MM TCEP)AND SET UP IN SITTING DROP IN A 1:2 RATIO WITH HAMPTON INDEX ...Details: PROTEIN WAS CONCENTRATED TO 12 MG/ML IN PURIFICATION BUFFER (10MM HEPES, 500MM NACL, 5% GLYCEROL, 10% GALACTOSE, 0.5MM TCEP)AND SET UP IN SITTING DROP IN A 1:2 RATIO WITH HAMPTON INDEX SCREEN - B8 (1.4M TRI-SODIUM CITRATE DIHYDRATE, 0.1M HEPES, PH 7.5). |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→37 Å / Num. obs: 49220 / % possible obs: 99.3 % / Observed criterion σ(I): 1.3 / Redundancy: 3.4 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.63→1.67 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ET6 Resolution: 1.63→37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.37 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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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: 12.388 Å2
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Refinement step | Cycle: LAST / Resolution: 1.63→37 Å
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Refine LS restraints |
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