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Yorodumi- PDB-2wz1: STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN SOLUBLE GUANYLATE CYCL... -
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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. | ||||||
Components | GUANYLATE CYCLASE SOLUBLE SUBUNIT BETA-1 | ||||||
Keywords | LYASE / GUCY1 / METAL-BINDING / CGMP BIOSYNTHESIS / NUCLEOTIDE-BINDING / CYCLASE / GUCY1B3 / GTP-BINDING | ||||||
Function / homology | Function and homology information 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 / cellular response to nitric oxide / cGMP-mediated signaling / Smooth Muscle Contraction / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | 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. | ||||||
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 | 2wz1.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wz1.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wz1_validation.pdf.gz | 446.3 KB | Display | wwPDB validaton report |
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Full document | 2wz1_full_validation.pdf.gz | 447.4 KB | Display | |
Data in XML | 2wz1_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 2wz1_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/2wz1 ftp://data.pdbj.org/pub/pdb/validation_reports/wz/2wz1 | HTTPS FTP |
-Related structure data
Related structure data | 3uvjC 3et6S 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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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: |
-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.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE2 / References: UniProt: Q02153, guanylate cyclase #2: Chemical | #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: 2.1 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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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