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Yorodumi- PDB-1xfy: Crystal structure of anthrax edema factor (EF) in complex with ca... -
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-Basic information
Entry | Database: PDB / ID: 1xfy | ||||||
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Title | Crystal structure of anthrax edema factor (EF) in complex with calmodulin | ||||||
Components |
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Keywords | LYASE/METAL BINDING PROTEIN / protein-protein interaction / LYASE-METAL BINDING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information calcium- and calmodulin-responsive adenylate cyclase activity / : / : / adenylate cyclase / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / cAMP biosynthetic process / adenylate cyclase activity / CaM pathway / Cam-PDE 1 activation ...calcium- and calmodulin-responsive adenylate cyclase activity / : / : / adenylate cyclase / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / cAMP biosynthetic process / adenylate cyclase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / regulation of synaptic vesicle endocytosis / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / host cell cytosol / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / response to corticosterone / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / small molecule binding / RHO GTPases activate PAKs / : / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / phosphatidylinositol 3-kinase binding / eNOS activation / enzyme regulator activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / response to amphetamine / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / positive regulation of nitric-oxide synthase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / response to calcium ion Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.3 Å | ||||||
Authors | Shen, Y. / Zhukovskaya, N.L. / Guo, Q. / Florian, J. / Tang, W.J. | ||||||
Citation | Journal: EMBO J. / Year: 2005 Title: Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor. Authors: Shen, Y. / Zhukovskaya, N.L. / Guo, Q. / Florian, J. / Tang, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xfy.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1xfy.ent.gz | 857.3 KB | Display | PDB format |
PDBx/mmJSON format | 1xfy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xfy_validation.pdf.gz | 603.5 KB | Display | wwPDB validaton report |
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Full document | 1xfy_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1xfy_validation.xml.gz | 263.2 KB | Display | |
Data in CIF | 1xfy_validation.cif.gz | 337.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/1xfy ftp://data.pdbj.org/pub/pdb/validation_reports/xf/1xfy | HTTPS FTP |
-Related structure data
Related structure data | 1xfuC 1xfvC 1xfwC 1xfxC 1xfzC 1y0vC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 90128.898 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: cya / Production host: Escherichia coli (E. coli) / References: UniProt: P40136, adenylate cyclase #2: Protein | Mass: 16851.561 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CA / |
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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: 2.1 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG400, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 190 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 28, 2003 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→50 Å / Num. obs: 113362 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.054 / Rsym value: 0.034 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 3.25→3.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.463 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 3.3→10 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 317018.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.2904 Å2 / ksol: 0.239208 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.3→3.5 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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