+Open data
-Basic information
Entry | Database: PDB / ID: 1bcz | ||||||
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Title | RECOMBINANT RAT ANNEXIN V, T72S MUTANT | ||||||
Components | ANNEXIN V | ||||||
Keywords | CALCIUM-BINDING PROTEIN / CALCIUM BINDING PROTEIN / PHOSPHOLIPID MEMBRANE BINDING PROTEIN | ||||||
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 / DIFFERENCE FOURIER / Resolution: 2.2 Å | ||||||
Authors | Mo, Y.D. / Swairjo, M.A. / Li, C.W. / Head, J.F. / Seaton, B.A. | ||||||
Citation | Journal: Biochemistry / Year: 1998 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bcz.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bcz.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 1bcz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bcz_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 1bcz_full_validation.pdf.gz | 443.7 KB | Display | |
Data in XML | 1bcz_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1bcz_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/1bcz ftp://data.pdbj.org/pub/pdb/validation_reports/bc/1bcz | HTTPS FTP |
-Related 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: 35774.434 Da / Num. of mol.: 1 / Mutation: T72S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P14668 | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SO4 / | #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: 2.47 Å3/Da / Density % sol: 50.12 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 14383 / % possible obs: 84.4 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 31 Å2 / Rsym value: 0.113 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 1.95 / Rsym value: 0.249 / % possible all: 39.9 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 14209 / % possible obs: 83.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.113 |
Reflection shell | *PLUS % possible obs: 39.9 % / Rmerge(I) obs: 0.249 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2.2→10 Å / Rfactor Rfree error: 0.011 / 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: 30.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.227 / Rfactor obs: 0.227 / Rfactor Rfree: 0.299 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.359 / Rfactor Rwork: 0.342 / Rfactor obs: 0.342 |