+Open data
-Basic information
Entry | Database: PDB / ID: 4oyp | ||||||
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Title | Human solAC Complexed with 1-Benzofuran-2-carboxylic acid | ||||||
Components | Adenylate cyclase type 10 | ||||||
Keywords | LYASE | ||||||
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 / Resolution: 2.28 Å | ||||||
Authors | Vinkovic, M. | ||||||
Citation | Journal: Chemmedchem / Year: 2014 Title: Crystal structure of human soluble adenylate cyclase reveals a distinct, highly flexible allosteric bicarbonate binding pocket. Authors: Saalau-Bethell, S.M. / Berdini, V. / Cleasby, A. / Congreve, M. / Coyle, J.E. / Lock, V. / Murray, C.W. / O'Brien, M.A. / Rich, S.J. / Sambrook, T. / Vinkovic, M. / Yon, J.R. / Jhoti, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oyp.cif.gz | 209.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oyp.ent.gz | 166.5 KB | Display | PDB format |
PDBx/mmJSON format | 4oyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oyp_validation.pdf.gz | 442.5 KB | Display | wwPDB validaton report |
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Full document | 4oyp_full_validation.pdf.gz | 448.3 KB | Display | |
Data in XML | 4oyp_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 4oyp_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/4oyp ftp://data.pdbj.org/pub/pdb/validation_reports/oy/4oyp | HTTPS FTP |
-Related structure data
Related structure data | 4oyaC 4oybC 4oyiC 4oymC 4oyoC 4oywC 4oyxC 4oyzC 4oz2C 4oz3C 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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-Components
#1: Protein | Mass: 53466.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADCY10, SAC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96PN6, adenylate cyclase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-BZ2 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 1ul of protein solution was mixed with 1ul of reservoir solution (0.1M sodium acetate, pH 4.8, 0.2M trisodium citrate, 16-18% PEG4K and 10% glycerol) and left to equilibrate at 4C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 22, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→28.68 Å / Num. obs: 23889 / % possible obs: 96.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 37.08 Å2 / Net I/σ(I): 10.9 |
-Processing
Software | Name: BUSTER / Version: 2.11.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.28→28.68 Å / Cor.coef. Fo:Fc: 0.9498 / Cor.coef. Fo:Fc free: 0.9109 / SU R Cruickshank DPI: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.311 / SU Rfree Blow DPI: 0.223 / SU Rfree Cruickshank DPI: 0.219
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Displacement parameters | Biso mean: 39.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.28→28.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.38 Å / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: 21.6683 Å / Origin y: 25.589 Å / Origin z: -0.5627 Å
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Refinement TLS group | Selection details: { A|0 - A|468 } |