+Open data
-Basic information
Entry | Database: PDB / ID: 3f39 | ||||||
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Title | Apoferritin: complex with phenol | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / 4-helix bundle / anesthetic / propofol analogue / phenol / 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 / FOURIER SYNTHESIS / Resolution: 1.85 Å | ||||||
Authors | Vedula, L.S. / Economou, N.J. / Rossi, M.J. / Eckenhoff, R.G. / Loll, P.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: A unitary anesthetic binding site at high resolution. Authors: Vedula, L.S. / Brannigan, G. / Economou, N.J. / Xi, J. / Hall, M.A. / Liu, R. / Rossi, M.J. / Dailey, W.P. / Grasty, K.C. / Klein, M.L. / Eckenhoff, R.G. / Loll, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f39.cif.gz | 53.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f39.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 3f39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f39_validation.pdf.gz | 446.9 KB | Display | wwPDB validaton report |
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Full document | 3f39_full_validation.pdf.gz | 447.4 KB | Display | |
Data in XML | 3f39_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 3f39_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/3f39 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/3f39 | HTTPS FTP |
-Related structure data
Related structure data | 3f32C 3f33C 3f34C 3f35C 3f36C 3f37C 3f38C 1xz1S 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
#1: Protein | Mass: 19872.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: spleen / References: UniProt: P02791 | ||||||
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#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-IPH / | #4: Chemical | #5: 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: 3.14 Å3/Da / Density % sol: 60.77 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Cadmium sulfate, ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20.97 Å / Num. all: 28612 / Num. obs: 28612 / % possible obs: 99.4 % / Observed criterion σ(I): 3.1 / Redundancy: 17.75 % / Biso Wilson estimate: 37.07 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 8.27 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2739 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1XZ1 Resolution: 1.85→20.97 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.312 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.111 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.963 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→20.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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