+Open data
-Basic information
Entry | Database: PDB / ID: 1xz3 | ||||||
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Title | Complex of apoferritin with isoflurane | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / 4-helix bundle | ||||||
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: 1.75 Å | ||||||
Authors | Liu, R. / Loll, P.J. / Eckenhoff, R.G. | ||||||
Citation | Journal: Faseb J. / Year: 2005 Title: Structural basis for high-affinity volatile anesthetic binding in a natural 4-helix bundle protein. Authors: Liu, R. / Loll, P.J. / Eckenhoff, R.G. | ||||||
History |
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Remark 999 | SEQUENCE Author states that residue 93 is indeed a LEU. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xz3.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xz3.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 1xz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xz3_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
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Full document | 1xz3_full_validation.pdf.gz | 443 KB | Display | |
Data in XML | 1xz3_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 1xz3_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/1xz3 ftp://data.pdbj.org/pub/pdb/validation_reports/xz/1xz3 | HTTPS FTP |
-Related structure data
Related structure data | 1xz1C 1gwgS C: citing same article (ref.) 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 on special symmetry positions |
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Details | Biological unit is 24-mer: x,y,z; -x,-y,z; -x,y,-z; x,-y,-z; z,x,y; z,-x,-y; -z,-x,y; -z,x,-y; y,z,x; -y,z,-x; y,-z,-x; -y,-z,x; y,x,-z; -y,-x,-z; y,-x,z; -y,x,z; x,z,-y; -x,z,y; -x,-z,-y; x,-z,y; z,y,-x; z,-y,x; -z,y,x; -z,-y,-x; |
-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-ICF / | #4: 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: 3.15 Å3/Da / Density % sol: 60.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: cadmium sulfate, HEPES, sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0722 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2004 Details: parabolic collimating mirror upstream of monochromator |
Radiation | Monochromator: parabolic collimating mirror upstream of monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0722 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→30 Å / Num. all: 25454 / Num. obs: 25454 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.74→1.82 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2551 / % possible all: 78.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1GWG Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.185 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.404 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.097 Å / Luzzati d res low obs: 0.098 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 28.5037 Å / Origin y: 9.6383 Å / Origin z: 39.6426 Å
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