+Open data
-Basic information
Entry | Database: PDB / ID: 1g5n | |||||||||
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Title | ANNEXIN V COMPLEX WITH HEPARIN OLIGOSACCHARIDES | |||||||||
Components | ANNEXIN V | |||||||||
Keywords | BLOOD CLOTTING / helix-bundle / membrane binding / heparin / heparan sulfate | |||||||||
Function / homology | Function and homology information negative regulation of prolactin secretion / cellular response to gonadotropin-releasing hormone / regulation of flagellated sperm motility / Platelet degranulation / endothelial microparticle / cellular response to lead ion / P-type calcium transporter activity / response to thyroid hormone / calcium-dependent phospholipid binding / negative regulation of blood coagulation ...negative regulation of prolactin secretion / cellular response to gonadotropin-releasing hormone / regulation of flagellated sperm motility / Platelet degranulation / endothelial microparticle / cellular response to lead ion / P-type calcium transporter activity / response to thyroid hormone / calcium-dependent phospholipid binding / negative regulation of blood coagulation / vesicle membrane / phosphatidylserine binding / peptide hormone binding / : / intercalated disc / axon terminus / cell projection / response to calcium ion / sarcolemma / receptor tyrosine kinase binding / synaptic vesicle membrane / Z disc / blood coagulation / synaptic vesicle / perikaryon / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / dendrite / calcium ion binding / extracellular space / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | |||||||||
Authors | Capila, I. / Heraiz, M.J. / Mo, Y.D. / Mealy, T.R. / Campos, B. / Dedman, J.R. / Linhardt, R.J. / Seaton, B.A. | |||||||||
Citation | Journal: Structure / Year: 2001 Title: Annexin V--heparin oligosaccharide complex suggests heparan sulfate--mediated assembly on cell surfaces. Authors: Capila, I. / Hernaiz, M.J. / Mo, Y.D. / Mealy, T.R. / Campos, B. / Dedman, J.R. / Linhardt, R.J. / Seaton, B.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g5n.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g5n.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 1g5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g5n_validation.pdf.gz | 521.1 KB | Display | wwPDB validaton report |
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Full document | 1g5n_full_validation.pdf.gz | 527 KB | Display | |
Data in XML | 1g5n_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 1g5n_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/1g5n ftp://data.pdbj.org/pub/pdb/validation_reports/g5/1g5n | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35657.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: LC5 / Plasmid: PKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P14668 | ||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CA / #4: 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: 2.45 Å3/Da / Density % sol: 49.76 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: soaking / pH: 8.2 Details: PEG 4000, calcium chloride, HEPES buffer, pH 8.2, soaking, temperature 290.0K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion / Details: Campos, B., (1998) Biochemistry, 37, 8004. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 25, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. all: 26655 / Num. obs: 24078 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 3 % / Rmerge(I) obs: 0.219 / % possible all: 93.5 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. obs: 26655 / Num. measured all: 144885 |
Reflection shell | *PLUS % possible obs: 93.5 % / Mean I/σ(I) obs: 10.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: Unpublished structure of wild-type annexin V Resolution: 1.9→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
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Refinement step | Cycle: LAST / Resolution: 1.9→100 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 100 Å / σ(F): 0 / Rfactor obs: 0.205 / Rfactor Rfree: 0.236 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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