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Open data
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Basic information
Entry | Database: PDB / ID: 1k0k | ||||||
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Title | Yeast Profilin, Cubic Crystal Form | ||||||
![]() | PROFILIN | ||||||
![]() | CONTRACTILE PROTEIN / ACTIN-BINDING PROTEIN / PIP2 BINDING PROTEIN / POLY-L-PROLINE BINDING PROTEIN | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Vorobiev, S. / Fedorov, A.A. / Almo, S.C. | ||||||
![]() | ![]() Title: A Comparative Structural Analysis of Profilins Authors: Vorobiev, S. / Fedorov, A.A. / Almo, S.C. #1: ![]() Title: Structure Determination and Characterization of Saccharomyces Cerevisae Profilin Authors: Eads, J.C. / Mahoney, N.M. / Vorobiev, S. / Bresnick, A.R. / Wen, K.K. / Rubenstein, P.A. / Haarer, B.K. / Almo, S.C. #2: ![]() Title: X-Ray Structures of Isoforms of the Actin-Binding Protein Profilin That Differ in their Affinity for Phosphatidylinositol Phosphates Authors: Fedorov, A.A. / Magnus, K.A. / Graupe, M.H. / Lattman, E.E. / Pollard, T.D. / Almo, S.C. #3: ![]() Title: Purification, Characterization and Crystallization of Human Platelet Profilin Expressed in Escherichia Coli Authors: Fedorov, A.A. / Pollard, T.D. / Almo, S.C. #4: ![]() Title: The Molecular Basis for Allergen Cross-Reactivity: Crystal Structure and Ige-Epitope Mapping of Birch Pollen Profilin Authors: Fedorov, A.A. / Ball, T. / Mahoney, N.M. / Valenta, R. / 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 | ![]() | 39.4 KB | Display | ![]() |
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PDB format | ![]() | 27 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 375.1 KB | Display | ![]() |
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Full document | ![]() | 377 KB | Display | |
Data in XML | ![]() | 4.4 KB | Display | |
Data in CIF | ![]() | 6.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1f2kC ![]() 1yprS S: Starting model for refinement C: citing same article ( |
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Similar 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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Details | The biological assembly is a monomer |
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Components
#1: Protein | Mass: 13559.190 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.165 Å3/Da / Density % sol: 79.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: sodium format, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→20 Å / Num. all: 14401 / Num. obs: 14401 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 45.3 |
Reflection shell | Resolution: 2.35→2.43 Å / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 12.9 / % possible all: 92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1YPR Resolution: 2.35→20 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: flat model / Bsol: 76.5199 Å2 / ksol: 0.391558 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.2 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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