+Open data
-Basic information
Entry | Database: PDB / ID: 4p2m | ||||||
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Title | Swapped Dimer of Mycobacterial Adenylyl cyclase Rv1625c: Form 1 | ||||||
Components | Adenylate cyclaseAdenylyl cyclase | ||||||
Keywords | LYASE / beta-alpha-beta sandwich / Domain swapping / Adenylyl cyclase / signal transduction | ||||||
Function / homology | Function and homology information receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase activity / cGMP biosynthetic process / 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 / guanylate cyclase activity / cGMP biosynthetic process / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 4p2m.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p2m.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 4p2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/4p2m ftp://data.pdbj.org/pub/pdb/validation_reports/p2/4p2m | HTTPS FTP |
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-Related structure data
Related structure data | 4p2fSC 4p2xC 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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Details | Monomer in solution confirmed by gel filtration |
-Components
#1: Protein | Mass: 25639.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cya, Rv1625c, MT1661, MTCY01B2.17c / Plasmid: p-PROEX-HT / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 References: UniProt: P0A4Y0, UniProt: P9WQ35*PLUS, adenylate cyclase #2: Chemical | #3: Chemical | ChemComp-PEG / #4: 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: 2.09 Å3/Da / Density % sol: 41.24 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 8.5 / Details: 0.2 M ammonium sulphate, Tris pH 8.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9762 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 4, 2011 / Details: bent collimating mirror and toroid |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→46.45 Å / Num. obs: 11639 / % possible obs: 100 % / Redundancy: 23 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 23 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 7.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4P2F Resolution: 2.7→37.28 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.875 / SU B: 10.915 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.072 / 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: 34.872 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→37.28 Å
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