+Open data
-Basic information
Entry | Database: PDB / ID: 1lqx | ||||||
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Title | Crystal structure of V45E mutant of cytochrome b5 | ||||||
Components | cytochrome b5 | ||||||
Keywords | ELECTRON TRANSPORT / CYTOCHROME B5 / TRYPSIN-CLEAVED FRAGMENT / MUTANT V45E | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Gan, J.-H. / Wu, J. / Wang, Z.-Q. / Wang, Y.-H. / Huang, Z.-X. / Xia, Z.-X. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structures of V45E and V45Y mutants and structure comparison of a variety of cytochrome b5 mutants. Authors: Gan, J.H. / Wu, J. / Wang, Z.Q. / Wang, Y.H. / Huang, Z.X. / Xia, Z.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lqx.cif.gz | 32.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lqx.ent.gz | 20.7 KB | Display | PDB format |
PDBx/mmJSON format | 1lqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/1lqx ftp://data.pdbj.org/pub/pdb/validation_reports/lq/1lqx | HTTPS FTP |
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-Related structure data
Related structure data | 1lr6C 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9505.362 Da / Num. of mol.: 1 / Fragment: trypsin-solubilized fragment of cytochrome b5 / Mutation: V45E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Organ: liver / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00171 |
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#2: Chemical | ChemComp-HEM / |
#3: 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: 2.74 Å3/Da / Density % sol: 55.09 % | ||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: PHOSPHATE BUFFER, pH 7.5, VAPOR DIFFUSION, temperature 293.0K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SEALED TUBE / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 12, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→22.91 Å / Num. obs: 9048 / % possible obs: 93.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.051 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.7 / % possible all: 74.5 |
Reflection | *PLUS Highest resolution: 1.8 Å / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 74.5 % / Rmerge(I) obs: 0.219 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1EHB Resolution: 1.8→22.91 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.3076 Å2 / ksol: 0.380321 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2
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Refine analyze | Luzzati coordinate error free: 0.23 Å / Luzzati sigma a free: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→22.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Rfactor all: 0.192 / Rfactor obs: 0.189 / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.355 / Rfactor Rwork: 0.271 |