+Open data
-Basic information
Entry | Database: PDB / ID: 1avc | ||||||
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Title | BOVINE ANNEXIN VI (CALCIUM-BOUND) | ||||||
Components | ANNEXIN VI | ||||||
Keywords | CALCIUM/PHOSPHOLIPID-BINDING PROTEIN / ANNEXIN / CALCIUM-BINDING / MEMBRANE-BINDING / CALCIUM-PHOSPHOLIPID-BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information negative regulation of sequestering of calcium ion / growth plate cartilage chondrocyte differentiation / biomineral tissue development / chondroitin sulfate binding / mitochondrial calcium ion homeostasis / chromaffin granule membrane / regulation of muscle contraction / plasma membrane repair / calcium-dependent phospholipid binding / calcium ion import ...negative regulation of sequestering of calcium ion / growth plate cartilage chondrocyte differentiation / biomineral tissue development / chondroitin sulfate binding / mitochondrial calcium ion homeostasis / chromaffin granule membrane / regulation of muscle contraction / plasma membrane repair / calcium-dependent phospholipid binding / calcium ion import / cargo receptor activity / neural crest cell migration / cholesterol binding / phosphatidylserine binding / mitochondrial crista / ligand-gated monoatomic ion channel activity / stress fiber / calcium ion transmembrane transport / apoptotic signaling pathway / calcium channel activity / calcium ion transport / calcium-dependent protein binding / actin filament binding / melanosome / heparin binding / vesicle / membrane => GO:0016020 / focal adhesion / calcium ion binding / GTP binding / perinuclear region of cytoplasm / enzyme binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Avila-Sakar, A.J. / Creutz, C.E. / Kretsinger, R.H. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 1998 Title: Crystal structure of bovine annexin VI in a calcium-bound state. Authors: Avila-Sakar, A.J. / Creutz, C.E. / Kretsinger, R.H. #1: Journal: Biochim.Biophys.Acta / Year: 1996 Title: The Crystal Structure of Annexin Vi Indicates Relative Rotation of the Two Lobes Upon Membrane Binding Authors: Kawasaki, H. / Avila-Sakar, A. / Creutz, C.E. / Kretsinger, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1avc.cif.gz | 140.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1avc.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 1avc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/1avc ftp://data.pdbj.org/pub/pdb/validation_reports/av/1avc | HTTPS FTP |
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-Related structure data
Related structure data | 1annS 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
#1: Protein | Mass: 76011.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cellular location: MEMBRANE-PERIPHERAL / Organ: LIVER / References: UniProt: P79134 | ||
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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: 2.99 Å3/Da / Density % sol: 39.7 % / Description: PROBE ~1/2 THE MASS OF ANNEXIN VI | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: VAPOUR DIFFUSION (HANGING DROP), SODIUM ACETATE 1.2 M AS PRECIPITANT, POTASSIUM CACODYLATE 0.1 M, PH 6.5, CALCIUM CHLORIDE 6.2 MM ROOM TEMPERATURE, vapor diffusion - hanging drop Temp details: room temp | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.0093 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Apr 14, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0093 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 30424 / % possible obs: 98.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.307 / % possible all: 99.3 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 10 Å / Num. obs: 19075 / % possible obs: 98.7 % / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 99.6 % / Redundancy: 3.8 % / Num. unique obs: 1912 / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 9.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: BOVINE ANNEXIN VI: PDB ENTRY 1ANN Resolution: 2.9→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT B=62.4 A**2, K=0.48
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Displacement parameters | Biso mean: 28.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 17821 / Num. reflection Rfree: 1157 / Rfactor obs: 0.204 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.329 / Rfactor obs: 0.285 |