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Yorodumi- PDB-6iqj: crystal structure of Arabidopsis thaliana Profilin 2 complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iqj | ||||||
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Title | crystal structure of Arabidopsis thaliana Profilin 2 complex with formin1 | ||||||
Components |
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Keywords | PLANT PROTEIN / actin binding / regulate actin network | ||||||
Function / homology | Function and homology information inflorescence development / lateral root development / actin nucleation / leaf development / sequestering of actin monomers / barbed-end actin filament capping / actin polymerization or depolymerization / cell wall / actin monomer binding / chloroplast ...inflorescence development / lateral root development / actin nucleation / leaf development / sequestering of actin monomers / barbed-end actin filament capping / actin polymerization or depolymerization / cell wall / actin monomer binding / chloroplast / defense response / actin filament binding / actin binding / cell cortex / actin cytoskeleton organization / membrane => GO:0016020 / cytoskeleton / endoplasmic reticulum / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.922 Å | ||||||
Authors | Qiao, Z. / Gao, Y. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Structural and computational examination of theArabidopsisprofilin-Poly-P complex reveals mechanistic details in profilin-regulated actin assembly. Authors: Qiao, Z. / Sun, H. / Ng, J.T.Y. / Ma, Q. / Koh, S.H. / Mu, Y. / Miao, Y. / Gao, Y.G. #1: Journal: To Be Published Title: Profilin 3 dynamictly regulate fomrin binding by its N terminal tail Authors: Qiao, Z. / Gao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iqj.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iqj.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 6iqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iqj_validation.pdf.gz | 437.3 KB | Display | wwPDB validaton report |
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Full document | 6iqj_full_validation.pdf.gz | 437.8 KB | Display | |
Data in XML | 6iqj_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 6iqj_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/6iqj ftp://data.pdbj.org/pub/pdb/validation_reports/iq/6iqj | HTTPS FTP |
-Related structure data
Related structure data | 6iqfC 6iqiC 6iqkC 3nulS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14010.833 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PFN2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q42418 #2: Protein/peptide | Mass: 1358.646 Da / Num. of mol.: 2 / Fragment: UNP residues 524-536 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SE97 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.73 % |
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Crystal grow | Temperature: 291.15 K / Method: evaporation Details: 0.1M Bis-tris (pH 7.0), 2.0M ammonium phosphate dibasic |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→40.414 Å / Num. obs: 18928 / % possible obs: 97.37 % / Redundancy: 10 % / CC1/2: 0.998 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.923→1.991 Å / Num. unique obs: 759 / CC1/2: 0.793 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NUL Resolution: 1.922→40.414 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.922→40.414 Å
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Refine LS restraints |
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LS refinement shell |
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