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- PDB-4wp8: Crystal structure of Adenylyl cyclase Ma1120 from Mycobacterium A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wp8 | ||||||
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Title | Crystal structure of Adenylyl cyclase Ma1120 from Mycobacterium Avium in complex with 2'5'-DD-3'-ATP and Manganese ion | ||||||
![]() | Ma1120 | ||||||
![]() | LYASE / Adenylyl cyclase / 2'5'-dd-3'-ATP | ||||||
Function / homology | ![]() adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / intracellular signal transduction / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barathy, D.V. / Bharambe, N.G. / Suguna, K. | ||||||
![]() | ![]() Title: Autoinhibitory mechanism and activity-related structural changes in a mycobacterial adenylyl cyclase Authors: Barathy, D.V. / Bharambe, N.G. / Syed, W. / Zaveri, A. / Visweswariah, S.S. / Cola sigmaf o, M. / Misquith, S. / Suguna, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88 KB | Display | ![]() |
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PDB format | ![]() | 63.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wp3SC ![]() 4wp9C ![]() 4wpaC 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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Unit cell |
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Components
#1: Protein | Mass: 19062.814 Da / Num. of mol.: 2 / Fragment: UNP residues 53-216 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.84 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 9.1 Details: 0.2M Sodium phosphate dibasic dihydrate, 20 % (w/v) Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 27, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95327 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→55.96 Å / Num. obs: 35884 / % possible obs: 99.78 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 3.1 / % possible all: 99.5 |
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Processing
Software | Name: REFMAC / Version: 5.8.0073 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 4WP3 Resolution: 1.65→55.96 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.031 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.104 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.557 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→55.96 Å
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Refine LS restraints |
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