+Open data
-Basic information
Entry | Database: PDB / ID: 3nul | ||||||
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Title | Profilin I from Arabidopsis thaliana | ||||||
Components | PROFILIN I | ||||||
Keywords | ACTIN BINDING PROTEIN / PROFILIN / CYTOSKELETON | ||||||
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 / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Thorn, K. / Christensen, H.E.M. / Shigeta, R. / Huddler, D. / Chua, N.-H. / Shalaby, L. / 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 | 3nul.cif.gz | 50.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nul.ent.gz | 35.5 KB | Display | PDB format |
PDBx/mmJSON format | 3nul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nul_validation.pdf.gz | 432.1 KB | Display | wwPDB validaton report |
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Full document | 3nul_full_validation.pdf.gz | 431.7 KB | Display | |
Data in XML | 3nul_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 3nul_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/3nul ftp://data.pdbj.org/pub/pdb/validation_reports/nu/3nul | 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: 14288.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cellular location: CELLULAR CYTOSKELETON / Production host: Escherichia coli (E. coli) / References: UniProt: Q42449 | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 34.69 % | |||||||||||||||||||||||||
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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: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95, 1.1 | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Mar 15, 1996 / Details: NI/RH MIRRORS | |||||||||
Radiation | Monochromator: CRYSTALLINE MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→30 Å / Num. obs: 32355 / % possible obs: 96 % / Observed criterion σ(I): 5 / Redundancy: 4.5 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.055 / Net I/σ(I): 18.2 | |||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.189 / % possible all: 78.8 | |||||||||
Reflection | *PLUS Num. measured all: 146788 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→8 Å / Data cutoff high absF: 4200000000 / Data cutoff low absF: 0 / Cross valid method: DURING REFINEMENT / σ(F): 2
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Displacement parameters | Biso mean: 11.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.67 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: 0.2049 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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