+Open data
-Basic information
Entry | Database: PDB / ID: 1u9m | ||||||
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Title | Crystal structure of F58W mutant of cytochrome b5 | ||||||
Components | Cytochrome b5 | ||||||
Keywords | ELECTRON TRANSPORT / hemoprotein / F58Y and F58W mutants / conformational changes / aromatic-aromatic interactions / structure-function relationship | ||||||
Function / homology | Function and homology information Vitamin C (ascorbate) metabolism / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / mitochondrial outer membrane / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Shan, L. / Lu, J.-X. / Gan, J.-H. / Wang, Y.-H. / Huang, Z.-X. / Xia, Z.-X. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of the F58W mutant of cytochrome b5: the mutation leads to multiple conformations and weakens stacking interactions. Authors: Shan, L. / Lu, J.X. / Gan, J.H. / Wang, Y.H. / Huang, Z.X. / Xia, Z.X. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u9m.cif.gz | 121.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u9m.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 1u9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u9m_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 1u9m_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 1u9m_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 1u9m_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/1u9m ftp://data.pdbj.org/pub/pdb/validation_reports/u9/1u9m | HTTPS FTP |
-Related structure data
Related structure data | 1u9uC 1ehbS 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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Unit cell |
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-Components
#1: Protein | Mass: 9514.416 Da / Num. of mol.: 6 / Fragment: trypsin-solubilized fragment / Mutation: F58W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PU19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00171 #2: Chemical | ChemComp-HEM / #3: 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: 2.34 Å3/Da / Density % sol: 52.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: phosphate buffer, dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97891 Å |
Detector | Detector: CCD / Date: Dec 2, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97891 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 45329 / Num. obs: 40502 / % possible obs: 87.3 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.095 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.571 / Num. unique all: 4494 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1EHB Resolution: 2→35.55 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 230984.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.8144 Å2 / ksol: 0.360604 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→35.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
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Xplor file |
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