+Open data
-Basic information
Entry | Database: PDB / ID: 2zur | ||||||
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Title | Crystal Structure of Rh(nbd)/apo-Fr | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / Acetylation / Iron / Iron storage / Metal-binding | ||||||
Function / homology | Function and homology information : / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Abe, S. / Hirata, K. / Ueno, T. / Shimizu, N. / Yamamoto, M. / Takata, M. / Watanabe, Y. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Polymerization of phenylacetylene by rhodium complexes within a discrete space of apo-ferritin Authors: Abe, S. / Hirata, K. / Ueno, T. / Morino, K. / Shimizu, N. / Yamamoto, M. / Takata, M. / Yashima, E. / Watanabe, Y. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zur.cif.gz | 58.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zur.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zur_validation.pdf.gz | 462.6 KB | Display | wwPDB validaton report |
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Full document | 2zur_full_validation.pdf.gz | 464.4 KB | Display | |
Data in XML | 2zur_validation.xml.gz | 12 KB | Display | |
Data in CIF | 2zur_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/2zur ftp://data.pdbj.org/pub/pdb/validation_reports/zu/2zur | HTTPS FTP |
-Related structure data
Related structure data | 1datS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules X
#1: Protein | Mass: 20066.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Plasmid: pMK2 / Production host: Escherichia coli (E. coli) / Strain (production host): Nova Blue / References: UniProt: P02791 |
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-Non-polymers , 5 types, 209 molecules
#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: 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: 3.09 Å3/Da / Density % sol: 60.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.5M ammonium sulfate, 10mM cadmium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.5334 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2006 |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.5334 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 24236 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 38.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 9.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DAT Resolution: 1.8→37.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.684 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.801 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→37.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.847 Å / Total num. of bins used: 20
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