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Yorodumi- PDB-4p2f: Monomeric form of a single mutant (F363R) of Mycobacterial Adenyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p2f | ||||||
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Title | Monomeric form of a single mutant (F363R) of Mycobacterial Adenylyl cyclase Rv1625c | ||||||
Components | Adenylate cyclaseAdenylyl cyclase | ||||||
Keywords | LYASE / Adenylyl cyclase / Single mutant / alpha/beta fold / Signal transduction | ||||||
Function / homology | Function and homology information receptor guanylyl cyclase signaling pathway / peptide receptor activity / cGMP biosynthetic process / guanylate cyclase activity / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / manganese ion binding / membrane => GO:0016020 / intracellular signal transduction ...receptor guanylyl cyclase signaling pathway / peptide receptor activity / cGMP biosynthetic process / guanylate cyclase activity / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / manganese ion binding / membrane => GO:0016020 / intracellular signal transduction / magnesium ion binding / ATP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Barathy, D.V. / Mattoo, R. / Visweswariah, S.S. / Suguna, K. | ||||||
Citation | Journal: Iucrj / Year: 2014 Title: New structural forms of a mycobacterial adenylyl cyclase Rv1625c. Authors: Barathy, D. / Mattoo, R. / Visweswariah, 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 | 4p2f.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p2f.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 4p2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/4p2f ftp://data.pdbj.org/pub/pdb/validation_reports/p2/4p2f | HTTPS FTP |
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-Related structure data
Related structure data | 4p2mC 4p2xC 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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Details | Gel filtration indicates dimer in solution |
-Components
#1: Protein | Mass: 29989.650 Da / Num. of mol.: 1 / Mutation: F363R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cya, Rv1625c, MT1661, MTCY01B2.17c / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P0A4Y0, UniProt: P9WQ35*PLUS, adenylate cyclase | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.47 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 5.5 Details: 0.15M Ammonium sulphate, 0.1M Bis-Tris pH 5.5, 30% PEG 10K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 24, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→40.58 Å / Num. obs: 12712 / % possible obs: 98.98 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.05→2.103 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.3 / % possible all: 97.65 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ET6. Resolution: 2.05→40.58 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.071 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 25.873 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→40.58 Å
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