+Open data
-Basic information
Entry | Database: PDB / ID: 1a0k | ||||||
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Title | PROFILIN I FROM ARABIDOPSIS THALIANA | ||||||
Components | PROFILIN | ||||||
Keywords | CYTOSKELETON / PROFILIN / ACTIN-BINDING | ||||||
Function / homology | Function and homology information inflorescence development / unidimensional cell growth / phragmoplast / lateral root development / leaf development / sequestering of actin monomers / plasmodesma / actin polymerization or depolymerization / actin monomer binding / defense response ...inflorescence development / unidimensional cell growth / phragmoplast / lateral root development / leaf development / sequestering of actin monomers / plasmodesma / actin polymerization or depolymerization / actin monomer binding / defense response / spindle / cell cortex / nucleolus / mitochondrion / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Shigeta Junior, R. / Huddler, D. / Lindberg, U. / Schutt, C.E. | ||||||
Citation | Journal: Structure / Year: 1997 Title: The crystal structure of a major allergen from plants. Authors: Thorn, K.S. / Christensen, H.E. / Shigeta, R. / Huddler, D. / Shalaby, L. / Lindberg, U. / Chua, N.H. / Schutt, C.E. #1: Journal: Plant J. / Year: 1996 Title: Arabidopsis Profilins are Functionally Similar to Yeast Profilins: Identification of a Vascular Bundle-Specific Profilin and a Pollen-Specific Profilin Authors: Christensen, H.E. / Ramachandran, S. / Tan, C.T. / Surana, U. / Dong, C.H. / Chua, N.H. #2: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Structure Determination of Bovine Profilin at 2.0 A Resolution Authors: Cedergren-Zeppezauer, E.S. / Goonesekere, N.C. / Rozycki, M.D. / Myslik, J.C. / Dauter, Z. / Lindberg, U. / Schutt, C.E. #3: Journal: Nature / Year: 1993 Title: The Structure of Crystalline Profilin-Beta-Actin Authors: Schutt, C.E. / Myslik, J.C. / Rozycki, M.D. / Goonesekere, N.C. / Lindberg, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a0k.cif.gz | 42.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a0k.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 1a0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a0k_validation.pdf.gz | 367.5 KB | Display | wwPDB validaton report |
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Full document | 1a0k_full_validation.pdf.gz | 368.9 KB | Display | |
Data in XML | 1a0k_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 1a0k_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/1a0k ftp://data.pdbj.org/pub/pdb/validation_reports/a0/1a0k | HTTPS FTP |
-Related structure data
Related structure data | 3nulSC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 14279.183 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: COLUMBIA / Cell line: BL21 / Cellular location: CELLULAR CYTOSKELETON / Gene: PFN / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q42449 |
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#2: 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: 1.9 Å3/Da / Density % sol: 22 % | |||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: 2.0 M AMMONIUM SULFATE, 0.1 M CITRATE PH 5.0, 10 MM DTT, 0.2 MM EDTA | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: YALE MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 5530 / % possible obs: 90.4 % / Observed criterion σ(I): 5 / Redundancy: 2.6 % / Biso Wilson estimate: 4.02 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 0.2176 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 10.13 / Rsym value: 0.129 / % possible all: 55.5 |
Reflection | *PLUS Num. measured all: 48373 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NUL Resolution: 2.2→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.0001 / Cross valid method: DURING REFINEMENT / σ(F): 2
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Displacement parameters | Biso mean: 12.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.238 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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