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Yorodumi- PDB-1wc5: Soluble adenylyl cyclase CyaC from S. platensis in complex with a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wc5 | ||||||
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Title | Soluble adenylyl cyclase CyaC from S. platensis in complex with alpha, beta-methylene-ATP in presence of bicarbonate | ||||||
Components | ADENYLATE CYCLASEAdenylyl cyclase | ||||||
Keywords | LYASE / CYCLASE / SOLUBLE ADENYLYL CYCLASE / CAMP SIGNALING | ||||||
Function / homology | Function and homology information cyclic nucleotide biosynthetic process / adenylate cyclase activity / histidine kinase / phosphorelay sensor kinase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | SPIRULINA PLATENSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Steegborn, C. / Litvin, T.N. / Levin, L.R. / Buck, J. / Wu, H. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2005 Title: Bicarbonate Activation of Adenylyl Cyclase Via Promotion of Catalytic Active Site Closure and Metal Recruitment Authors: Steegborn, C. / Litvin, T.N. / Levin, L.R. / Buck, J. / Wu, H. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wc5.cif.gz | 169 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wc5.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 1wc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/1wc5 ftp://data.pdbj.org/pub/pdb/validation_reports/wc/1wc5 | HTTPS FTP |
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-Related structure data
Related structure data | 1wc0SC 1wc1C 1wc3C 1wc4C 1wc6C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24189.678 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 1005-1202 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SPIRULINA PLATENSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32393, adenylate cyclase #2: Chemical | ChemComp-APC / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Sequence details | THE PROTEIN WAS EXPRESSED WITH N-TERMNAL HIS-TAG CONSTRUCT COMPRISING OF RESIDUES MARKED AS 984- ...THE PROTEIN WAS EXPRESSED WITH N-TERMNAL HIS-TAG CONSTRUCT COMPRISING | |
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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: 2.08 Å3/Da / Density % sol: 40.93 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9785 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 33968 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WC0 Resolution: 2.3→14.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 385254.02 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.2733 Å2 / ksol: 0.321406 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→14.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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