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Yorodumi- PDB-3sn2: Crystal structure analysis of iron regulatory protein 1 in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sn2 | ||||||
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Title | Crystal structure analysis of iron regulatory protein 1 in complex with transferrin receptor IRE B RNA | ||||||
Components |
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Keywords | LYASE/RNA / RNA binding / iron sulfur cluster binding / phosphorylation / LYASE-RNA complex | ||||||
Function / homology | Function and homology information aconitate hydratase / aconitate hydratase activity / iron-responsive element binding / citrate metabolic process / response to iron(II) ion / tricarboxylic acid cycle / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Volz, K. / Selezneva, A.I. / Walden, W.E. | ||||||
Citation | Journal: Febs Lett. / Year: 2012 Title: Accommodating variety in iron-responsive elements: Crystal structure of transferrin receptor 1 B IRE bound to iron regulatory protein 1. Authors: Walden, W.E. / Selezneva, A. / Volz, K. #1: Journal: Science / Year: 2006 Title: Structure of dual function iron regulatory protein 1 complexed with ferritin IRE-RNA. Authors: Walden, W.E. / Selezneva, A.I. / Dupuy, J. / Volbeda, A. / Fontecilla-Camps, J.C. / Theil, E.C. / Volz, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sn2.cif.gz | 350.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sn2.ent.gz | 281 KB | Display | PDB format |
PDBx/mmJSON format | 3sn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/3sn2 ftp://data.pdbj.org/pub/pdb/validation_reports/sn/3sn2 | HTTPS FTP |
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-Related structure data
Related structure data | 2ipy S: Starting model for refinement |
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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: 100776.734 Da / Num. of mol.: 1 / Mutation: C437S/C503S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ACO1, FRP, IREB1, IREBP, IRP1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5465 / References: UniProt: Q01059, aconitate hydratase |
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#2: RNA chain | Mass: 9245.521 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
Sequence details | THE AUTHORS STATE THAT THE SEQUENCE PROVIDED FOR CHAINS A AND B IS CORRECT. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.56 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.7 M sodium citrate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 6, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.99→32.7 Å / Num. all: 30782 / Num. obs: 30703 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 106.1 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 11.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IPY 2ipy Resolution: 2.99→32.643 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 33.33 / 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 / Bsol: 95.345 Å2 / ksol: 0.406 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.99→32.643 Å
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Refine LS restraints |
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LS refinement shell |
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