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Yorodumi- PDB-4clk: Crystal structure of human soluble Adenylyl Cyclase in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 4clk | ||||||
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Title | Crystal structure of human soluble Adenylyl Cyclase in complex with alpha,beta-methyleneadenosine-5'-triphosphate | ||||||
Components | ADENYLATE CYCLASE TYPE 10 | ||||||
Keywords | LYASE / ADENOSINE-3'\ / 5'-CYCLIC-MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE | ||||||
Function / homology | Function and homology information negative regulation of cardiac muscle cell contraction / mitochondrial ATP transmembrane transport / epithelial cilium movement involved in extracellular fluid movement / bicarbonate binding / astrocyte end-foot / neuron projection retraction / : / central region of growth cone / positive regulation of glycogen catabolic process / glucose catabolic process ...negative regulation of cardiac muscle cell contraction / mitochondrial ATP transmembrane transport / epithelial cilium movement involved in extracellular fluid movement / bicarbonate binding / astrocyte end-foot / neuron projection retraction / : / central region of growth cone / positive regulation of glycogen catabolic process / glucose catabolic process / regulation of mitophagy / positive regulation of vascular associated smooth muscle cell apoptotic 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 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 / ATPase binding / manganese ion 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: 2.2 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 | 4clk.cif.gz | 198.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4clk.ent.gz | 156.6 KB | Display | PDB format |
PDBx/mmJSON format | 4clk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4clk_validation.pdf.gz | 803.8 KB | Display | wwPDB validaton report |
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Full document | 4clk_full_validation.pdf.gz | 809.9 KB | Display | |
Data in XML | 4clk_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 4clk_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/4clk ftp://data.pdbj.org/pub/pdb/validation_reports/cl/4clk | HTTPS FTP |
-Related structure data
Related structure data | 4clfSC 4cllC 4clpC 4clsC 4cltC 4cluC 4clwC 4clyC 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
-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 , 6 types, 175 molecules
#2: Chemical | ChemComp-APC / | ||||
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#3: Chemical | ChemComp-CL / | ||||
#4: Chemical | ChemComp-CA / | ||||
#5: Chemical | #6: Chemical | #7: 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: 4 Details: 100 MM PHOSPHATE/CITRATE PH 4.2, 200 MM NACL, 24 % (W/V) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 |
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: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.77 Å / Num. obs: 28304 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CLF Resolution: 2.2→86.82 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.49 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.201 / 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: 35.024 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→86.82 Å
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