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Yorodumi- PDB-4wp8: Crystal structure of Adenylyl cyclase Ma1120 from Mycobacterium A... -
+Open data
-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 | ||||||
Components | Ma1120 | ||||||
Keywords | LYASE / Adenylyl cyclase / 2'5'-dd-3'-ATP | ||||||
Function / homology | Function and homology information adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / intracellular signal transduction / metal ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium avium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Barathy, D.V. / Bharambe, N.G. / Suguna, K. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wp8.cif.gz | 88 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wp8.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 4wp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wp8_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4wp8_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4wp8_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 4wp8_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/4wp8 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/4wp8 | HTTPS FTP |
-Related structure data
Related structure data | 4wp3SC 4wp9C 4wpaC 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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-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.) Mycobacterium avium (bacteria) / Strain: TN 104 / Gene: cya1120 / Plasmid: pPROExHT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5UFR5, adenylate cyclase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95327 Å |
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 |
-Processing
Software | Name: REFMAC / Version: 5.8.0073 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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