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Yorodumi- PDB-2if4: Crystal structure of a multi-domain immunophilin from Arabidopsis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2if4 | ||||||
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Title | Crystal structure of a multi-domain immunophilin from Arabidopsis thaliana | ||||||
Components | ATFKBP42 | ||||||
Keywords | SIGNALING PROTEIN / FKBP-like / alpha-beta / TPR-like / alpha | ||||||
Function / homology | Function and homology information leaf development / auxin-activated signaling pathway / vacuolar membrane / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calmodulin binding / endoplasmic reticulum / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.85 Å | ||||||
Authors | Granzin, J. / Eckhoff, A. / Weiergraeber, O.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Crystal Structure of a Multi-domain Immunophilin from Arabidopsis thaliana: A Paradigm for Regulation of Plant ABC Transporters. Authors: Granzin, J. / Eckhoff, A. / Weiergraber, O.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2if4.cif.gz | 63 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2if4.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 2if4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/2if4 ftp://data.pdbj.org/pub/pdb/validation_reports/if/2if4 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 38364.395 Da / Num. of mol.: 1 / Fragment: FKBP-type domain and TPR domain, residues 1-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Ecotype Columbia / Gene: FKBP42, TWD1, UCU2 / Plasmid: PET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9LDC0 |
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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: 2.65 Å3/Da / Density % sol: 53.64 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 2.3 M ammonium sulfate, 2% (v/v) PEG 400, 0.1 M Hepes, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2004 / Details: Mirrors |
Radiation | Monochromator: Diamond, Germanium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→20 Å / Num. all: 9813 / Num. obs: 9813 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 88.3 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.059 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.85→2.92 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.6 / Num. unique all: 694 / Rsym value: 0.502 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.85→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 63.56 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.513 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→20 Å
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Refine LS restraints |
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