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Yorodumi- PDB-4usv: Crystal structure of human soluble Adenylyl Cyclase with pyrophos... -
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-Basic information
Entry | Database: PDB / ID: 4usv | ||||||
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Title | Crystal structure of human soluble Adenylyl Cyclase with pyrophosphate resulting from soaking with ATP and Calcium | ||||||
Components | ADENYLATE CYCLASE TYPE 10 | ||||||
Keywords | LYASE / REACTION PRODUCT | ||||||
Function / homology | Function and homology information negative regulation of cardiac muscle cell contraction / astrocyte end-foot / mitochondrial ATP transmembrane transport / epithelial cilium movement involved in extracellular fluid movement / bicarbonate binding / regulation of mitophagy / neuron projection retraction / positive regulation of glycogen catabolic process / central region of growth cone / cellular response to inorganic substance ...negative regulation of cardiac muscle cell contraction / astrocyte end-foot / mitochondrial ATP transmembrane transport / epithelial cilium movement involved in extracellular fluid movement / bicarbonate binding / regulation of mitophagy / neuron projection retraction / positive regulation of glycogen catabolic process / central region of growth cone / cellular response to inorganic substance / glucose catabolic process / regulation of membrane repolarization / adenylate cyclase / basal part of cell / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cAMP biosynthetic process / positive regulation of ossification / adenylate cyclase activity / positive regulation of protein targeting to mitochondrion / positive regulation of reactive oxygen species biosynthetic process / neuron projection extension / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of mitochondrial depolarization / positive regulation of ATP biosynthetic process / positive regulation of cardiac muscle hypertrophy / positive regulation of cardiac muscle cell apoptotic process / spermatid development / negative regulation of mitochondrial membrane potential / positive regulation of axon extension / Hedgehog 'off' state / negative regulation of reactive oxygen species biosynthetic process / neuron projection maintenance / positive regulation of peptidyl-threonine phosphorylation / cilium / manganese ion binding / ATPase binding / cytoskeleton / intracellular signal transduction / apical plasma membrane / dendrite / neuronal cell body / perinuclear region of cytoplasm / magnesium ion binding / mitochondrion / extracellular region / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kleinboelting, S. / Steegborn, C. | ||||||
Citation | Journal: FEBS J. / Year: 2014 Title: Structural Analysis of Human Soluble Adenylyl Cyclase and Crystal Structures of its Nucleotide Complexes -Implications for Cyclase Catalysis and Evolution. Authors: Kleinbolting, S. / Van Den Heuvel, J. / Steegborn, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4usv.cif.gz | 198.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4usv.ent.gz | 158.7 KB | Display | PDB format |
PDBx/mmJSON format | 4usv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/4usv ftp://data.pdbj.org/pub/pdb/validation_reports/us/4usv | HTTPS FTP |
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-Related structure data
Related structure data | 4ustC 4usuC 4uswC 4clkS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 54269.664 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-469 Source method: isolated from a genetically manipulated source Details: BETA-MERCAPTOETHANOL MODIFICATION AT RESIDUE CYS253 Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVL1392 / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q96PN6, adenylate cyclase |
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-Non-polymers , 7 types, 192 molecules
#2: Chemical | ChemComp-CL / | ||||||||
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#3: Chemical | ChemComp-CA / | ||||||||
#4: Chemical | #5: Chemical | ChemComp-ACT / | #6: Chemical | ChemComp-POP / | #7: Chemical | ChemComp-GOL / | #8: 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: 2.4 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 6 Details: 0.1 M SODIUM ACETATE PH 4.8, 0.2 M TRI-SODIUM-CITRATE, 15% (W/V) PEG 4000, 10% (V/V) GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91705 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2013 / Details: COLLIMATOR |
Radiation | Monochromator: SI111-DCM WITH SAGITTAL BENDER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91705 Å / Relative weight: 1 |
Reflection | Resolution: 2→87.36 Å / Num. obs: 37919 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.11 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CLK Resolution: 2→87.36 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.852 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 43.485 Å2
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Refinement step | Cycle: LAST / Resolution: 2→87.36 Å
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