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Open data
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Basic information
Entry | Database: PDB / ID: 1ypr | ||||||
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Title | SACCHAROMYCES CEREVISIAE (YEAST) PROFILIN | ||||||
![]() | PROFILIN | ||||||
![]() | ACTIN-BINDING PROTEIN / PROFILIN / CYTOSKELETON | ||||||
Function / homology | ![]() positive regulation of formin-nucleated actin cable assembly / mitotic actomyosin contractile ring assembly / sequestering of actin monomers / proline-rich region binding / actin monomer binding / intracellular transport / phosphatidylinositol-4,5-bisphosphate binding / cell cortex / cytoskeleton / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Eads, J.C. / Mahoney, N.M. / Almo, S.C. | ||||||
![]() | ![]() Title: Structure determination and characterization of Saccharomyces cerevisiae profilin Authors: Eads, J.C. / Mahoney, N.M. / Vorobiev, S. / Haarer, B.K. / Almo, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.1 KB | Display | ![]() |
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PDB format | ![]() | 43.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 374.3 KB | Display | ![]() |
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Full document | ![]() | 377.1 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 9.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.427531, 0.806755, -0.407876), Vector: |
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Components
#1: Protein | Mass: 13559.190 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: 1.0 M LI SULFATE, 0.1 M TRIS, PH 8.5, 0.01M NICL2 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→99 Å / Num. obs: 12068 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.064 / Net I/σ(I): 10.75 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 2.75 / Rsym value: 0.213 / % possible all: 77.5 |
Reflection | *PLUS Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS Lowest resolution: 2.4 Å / % possible obs: 77.5 % / Rmerge(I) obs: 0.213 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: ACANTHAMOEBA PROFILIN P1 Resolution: 2.3→25 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 34.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS, IN EARLY STAGES OF REFINEMENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 8
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.286 |