+Open data
-Basic information
Entry | Database: PDB / ID: 5hqo | ||||||
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Title | Crystal structure of IrCp*/I-Pd(allyl)-apo-rHLFr | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / IRON STORAGE | ||||||
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: 1.81 Å | ||||||
Authors | Maity, B. / Fukumori, K. / Abe, S. / Ueno, T. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2016 Title: Immobilization of two organometallic complexes into a single cage to construct protein-based microcompartments Authors: Maity, B. / Fukumori, K. / Abe, S. / Ueno, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hqo.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hqo.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 5hqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hqo_validation.pdf.gz | 463 KB | Display | wwPDB validaton report |
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Full document | 5hqo_full_validation.pdf.gz | 463.9 KB | Display | |
Data in XML | 5hqo_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 5hqo_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/5hqo ftp://data.pdbj.org/pub/pdb/validation_reports/hq/5hqo | HTTPS FTP |
-Related structure data
Related structure data | 5e1uC 5e2dC 1datS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19872.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Plasmid: pMK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02791 |
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-Non-polymers , 7 types, 114 molecules
#2: Chemical | #3: Chemical | ChemComp-PLL / | #4: Chemical | ChemComp-IR / #5: Chemical | ChemComp-CD / | #6: Chemical | ChemComp-SO4 / | #7: Chemical | #8: 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: 3.1 Å3/Da / Density % sol: 60.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulphate, Cadmium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.104 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.104 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→23 Å / Num. obs: 23629 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 59.97 |
Reflection shell | Resolution: 1.81→1.84 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 11.93 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAT Resolution: 1.81→21.93 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.881 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.115 Å2
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Refinement step | Cycle: 1 / Resolution: 1.81→21.93 Å
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Refine LS restraints |
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