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Open data
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Basic information
Entry | Database: PDB / ID: 1bcy | ||||||
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Title | RECOMBINANT RAT ANNEXIN V, T72K MUTANT | ||||||
![]() | ANNEXIN V | ||||||
![]() | CALCIUM-BINDING PROTEIN / CALCIUM BINDING PROTEIN / PHOSPHOLIPID MEMBRANE BINDING PROTEIN | ||||||
Function / homology | ![]() 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 / phosphatidylserine binding / peptide hormone binding / intercalated disc / axon terminus / : / cell projection / receptor tyrosine kinase binding / sarcolemma / synaptic vesicle membrane / Z disc / response to calcium ion / blood coagulation / synaptic vesicle / perikaryon / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / calcium ion binding / dendrite / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Mo, Y.D. / Swairjo, M.A. / Li, C.W. / Head, J.F. / Seaton, B.A. | ||||||
![]() | ![]() Title: Mutational and crystallographic analyses of interfacial residues in annexin V suggest direct interactions with phospholipid membrane components. Authors: Campos, B. / Mo, Y.D. / Mealy, T.R. / Li, C.W. / Swairjo, M.A. / Balch, C. / Head, J.F. / Retzinger, G. / Dedman, J.R. / Seaton, B.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.1 KB | Display | ![]() |
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PDB format | ![]() | 58.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.5 KB | Display | ![]() |
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Full document | ![]() | 444.3 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 35816.535 Da / Num. of mol.: 1 / Mutation: T72K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.2 Details: PROTEIN CRYSTALLIZED FROM AMMONIUM SULFATE, 20MM CACL2, 50MM HEPPS, PH 8.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→100 Å / Num. obs: 23032 / % possible obs: 85 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.098 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.92→1.99 Å / Redundancy: 1.12 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.34 / % possible all: 38.8 |
Reflection | *PLUS Highest resolution: 1.95 Å / Num. obs: 21238 / % possible obs: 84.9 % / Rmerge(I) obs: 0.098 |
Reflection shell | *PLUS % possible obs: 38.8 % / Rmerge(I) obs: 0.34 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 1.95→10 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 25.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.04 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.222 / Rfactor obs: 0.222 / Rfactor Rfree: 0.292 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.402 / Rfactor Rwork: 0.351 / Rfactor obs: 0.351 |