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Yorodumi- PDB-4cly: Crystal structure of human soluble Adenylyl Cyclase soaked with b... -
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-Basic information
Entry | Database: PDB / ID: 4cly | ||||||
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Title | Crystal structure of human soluble Adenylyl Cyclase soaked with biselenite | ||||||
Components | ADENYLATE CYCLASE TYPE 10 | ||||||
Keywords | LYASE / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information negative regulation of cardiac muscle cell contraction / astrocyte end-foot / mitochondrial ATP transmembrane transport / bicarbonate binding / epithelial cilium movement involved in extracellular fluid movement / neuron projection retraction / positive regulation of glycogen catabolic process / : / central region of growth cone / glucose catabolic process ...negative regulation of cardiac muscle cell contraction / astrocyte end-foot / mitochondrial ATP transmembrane transport / bicarbonate binding / epithelial cilium movement involved in extracellular fluid movement / neuron projection retraction / positive regulation of glycogen catabolic process / : / central region of growth cone / glucose catabolic process / regulation of mitophagy / 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 / negative regulation of mitochondrial membrane potential / spermatid development / 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 / neuronal cell body / dendrite / perinuclear region of cytoplasm / magnesium ion binding / mitochondrion / extracellular region / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Kleinboelting, S. / Weyand, M. / Steegborn, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Crystal Structures of Human Soluble Adenylyl Cyclase Reveal Mechanisms of Catalysis and of its Activation Through Bicarbonate. Authors: Kleinboelting, S. / Diaz, A. / Moniot, S. / Van Den Heuvel, J. / Weyand, M. / Levin, L.R. / Buck, J. / Steegborn, C. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cly.cif.gz | 200.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cly.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 4cly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cly_validation.pdf.gz | 472.3 KB | Display | wwPDB validaton report |
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Full document | 4cly_full_validation.pdf.gz | 476.9 KB | Display | |
Data in XML | 4cly_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 4cly_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/4cly ftp://data.pdbj.org/pub/pdb/validation_reports/cl/4cly | HTTPS FTP |
-Related structure data
Related structure data | 4clfSC 4clkC 4cllC 4clpC 4clsC 4cltC 4cluC 4clwC 4clzC 4cm0C 4cm2C 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 on special symmetry positions |
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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 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 , 5 types, 269 molecules
#2: Chemical | ChemComp-BSY / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-GOL / | #6: 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: 2.75 Å3/Da / Density % sol: 55 % / 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: 0.97626 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2012 / Details: COLLIMATOR |
Radiation | Monochromator: SI111-DCM WITH SAGITTAL BENDER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→48.79 Å / Num. obs: 68658 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CLF Resolution: 2.05→86.75 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.271 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.143 / 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: 38.619 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→86.75 Å
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Refine LS restraints |
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