+Open data
-Basic information
Entry | Database: PDB / ID: 5a1m | ||||||
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Title | Crystal structure of calcium-bound human adseverin domain A3 | ||||||
Components | ADSEVERIN | ||||||
Keywords | ACTIN-BINDING PROTEIN / ACTIN | ||||||
Function / homology | Function and homology information positive regulation of secretion / regulation of chondrocyte differentiation / 1-phosphatidylinositol binding / actin nucleation / positive regulation of megakaryocyte differentiation / positive regulation of actin nucleation / sequestering of actin monomers / actin filament severing / calcium-ion regulated exocytosis / actin filament capping ...positive regulation of secretion / regulation of chondrocyte differentiation / 1-phosphatidylinositol binding / actin nucleation / positive regulation of megakaryocyte differentiation / positive regulation of actin nucleation / sequestering of actin monomers / actin filament severing / calcium-ion regulated exocytosis / actin filament capping / barbed-end actin filament capping / actin polymerization or depolymerization / cell projection assembly / podosome / anchoring junction / phosphatidylserine binding / brush border / phosphatidylinositol-4,5-bisphosphate binding / central nervous system development / cell projection / actin filament binding / actin cytoskeleton / actin binding / cell cortex / positive regulation of apoptotic process / negative regulation of cell population proliferation / calcium ion binding / extracellular exosome / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Chumnarnsilpa, S. / Robinson, R.C. / Grimes, J.M. / Leyrat, C. | ||||||
Citation | Journal: Nat.Commun. / Year: 2015 Title: Calcium-Controlled Conformational Choreography in the N-Terminal Half of Adseverin. Authors: Chumnarnsilpa, S. / Robinson, R.C. / Grimes, J.M. / Leyrat, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a1m.cif.gz | 58.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a1m.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 5a1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/5a1m ftp://data.pdbj.org/pub/pdb/validation_reports/a1/5a1m | HTTPS FTP |
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-Related structure data
Related structure data | 5a1kC 1rgiS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11927.733 Da / Num. of mol.: 1 / Fragment: DOMAIN A3, RESIDUES 247-350 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSY5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q9Y6U3 |
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#2: Chemical | ChemComp-CA / |
#3: 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: 3.17 Å3/Da / Density % sol: 61.24 % / Description: NONE |
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Crystal grow | Details: 30 % POLYETHYLENE GLYCOL 6000, 100 MM HEPES PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→35.5 Å / Num. obs: 13860 / % possible obs: 100 % / Observed criterion σ(I): 3.5 / Redundancy: 14.2 % / Biso Wilson estimate: 20.36 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 3.5 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RGI RESIDUES 271-364 Resolution: 1.81→35.47 Å / Cor.coef. Fo:Fc: 0.9434 / Cor.coef. Fo:Fc free: 0.9439 / SU R Cruickshank DPI: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.099 / SU Rfree Cruickshank DPI: 0.092 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=997. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=997. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=1.
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Displacement parameters | Biso mean: 23.86 Å2
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Refine analyze | Luzzati coordinate error obs: 0.203 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→35.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.96 Å / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: 31.0636 Å / Origin y: 30.7887 Å / Origin z: 16.325 Å
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Refinement TLS group | Selection details: { A|* } |